Table of Contents - BioRuby API documentation
Pages
-
KNOWN_ISSUES
- KNOWN_ISSUES.rdoc - Known issues and bugs in BioRuby
- Known issues and bugs in BioRuby
- 1. Ruby version specific issues
- String encodings
- End-of-life Ruby versions
- Ruby 1.9.0
- Ruby 1.9.1 or earlier (including Ruby 1.8.7)
- Ruby 1.8.2 or earlier
- Problem with REXML DoS vulnerability patch before 09-Nov-2008
- RubyGems 0.8.11 or earlier
- JRuby
- Rubinius
- 2. OS and/or architecture-dependent issues
- Microsoft Windows
- Text mode issues
- String escaping of command-line arguments
- Windows 95/98/98SE/ME
- OpenVMS, BeOS, OS/2, djgpp, Windows CE
- 3. Known issues and bugs in BioRuby
- Bio::UniProtKB
- Bio::PDB
- Bio::Blast::Report
- Bio::Blast::Default::Report
- 4. Compatibility issues with other libraries/extensions
- Ruby on Rails
- 5. Historical descriptions
- CVS
-
README
- BioRuby
- FOR MORE INFORMATION
- Documents in this distribution
- Release notes, important changes and issues
- Tutorials and other useful information
- BioRuby development
- Documents written in Japanese
- Sample codes
- WWW
- WHERE TO OBTAIN
- WWW
- RubyGems
- git
- REQUIREMENTS
- OPTIONAL REQUIREMENTS
- INSTALL
- INSTALL by using RubyGems (recommended)
- Running self-test
- SETUP
- USAGE
- PLUGIN (Biogem)
- Recommended Plugins (gems)
- LICENSE
- REFERENCE
- CONTACT
-
README_DEV
- README.DEV
- HOW TO CONTRIBUTE TO THE BIORUBY PROJECT?
- Git
- Preparation before sending patches or pull requests
- Sending your contribution
- With patches
- With pull requests
- Notes for the treatment of contributions in the blessed repository
- Merging policy
- Git commit management policy
- LICENSE
- CODING STYLE
- Use the following naming conventions
- Indentation must not include tabs
- Parenthesis in the method definition line should be written
- Comments
- Documentation should be written in the RDoc format in the source code
- Standard documentation
- of files
- of classes and methods within those files
- Exception handling
- Testing code should use ‘test/unit’
- Using autoload
- NAMESPACE
- MAINTENANCE
- RUBY VERSION and IMPLEMENTATION
- OS and ARCHITECTURE
-
RELEASE_NOTES
- BioRuby 2.0.5 RELEASE NOTES
- Fixes
- Changes for developers
- Changes of CI (Continuous Integration)
- Changes of Gemfile and related files
- Others
- BioRuby 2.0.4 RELEASE NOTES
- Fixes
- BioRuby 2.0.3 RELEASE NOTES
- Bug fixes
- Incompatible changes
- Bio::Sequence::* incompatible changes since Ruby 3.0.0
- BioRuby 2.0.2 RELEASE NOTES
- Bug fixes
- Known issues
- BioRuby 2.0.1 RELEASE NOTES
- Bug fixes
- Improvement of sample scripts
- CWL (Common Workflow Language) workflow files are added
- BioRuby 2.0.0 RELEASE NOTES
- Features moved to separete gems
- BioRuby Shell is moved to “bio-shell”
- Executable files are moved to “bio-executables”
- Fast BLAST XML result parser by using Expat XML Parser is moved to “bio-blast-xmlparser”
- Bio::PhyloXML is moved to “bioruby-phyloxml”
- Bio::SQL is moved to “bio-biosql”
- New features and improvements
- HTTPS is used to access NCBI web services
- KEGG::GENES#diseases and related methods are added
- Pre-calculated ambiguity codon tables in Bio::CodonTable
- Bug fixes
- Incompatible changes
- Bio::Taxonomy is removed and merged to Bio::PhyloXML::Taxonomy
- Some features are moved to separete gems
- Known issues
- Other important news
- Ruby 1.8 is no longer supported
- Installation without RubyGems is no longer supported
-
Changes-1.3
- Incompatible and important changes since the BioRuby 1.2.1 release
- New features
- Support for sequence output with improvements of Bio::Sequence
- BioSQL support
- Bio::Blast
- Bio::GFF::GFF2 and Bio::GFF::GFF3
- Bio::Hinv
- Bio::NCBI::REST
- Bio::PAML::Codeml and Bio::PAML::Codeml::Report
- Bio::Locations
- Bio::TogoWS::REST
- Deprecated classes
- Bio::Features
- Bio::References
- Incompatible changes
- Bio::BIORUBY_VERSION
- Bio::Sequence
- Bio::Locations and Bio::Location
- Bio::Blast
- Bio::Blast::Default::Report and Bio::Blast::WU::Report
- Bio::Blat
- Bio::GFF, Bio::GFF::GFF2 and Bio::GFF::GFF3
- Bio::GFF::GFF2 and Bio::GFF::GFF3
- Bio::GFF::GFF2
- Bio::GFF::GFF3
- Bio::Pathway
- Bio::SQL and BioSQL related classes
-
RELEASE_NOTES-1.4.0
- BioRuby 1.4.0 RELEASE NOTES
- New features
- PhyloXML support
- FASTQ file format support
- DNA chromatogram support
- MEME (motif-based sequence analysis tools) support
- Improvement of KEGG parser classes
- Many sample scripts are added
- Unit tests can test installed BioRuby
- Deprecated features
- ChangeLog is replaced by git log
- “if __FILE__ == $0” convention
- Incompatible changes
- Bio::NCBI::REST
- Bio::KEGG
- dblinks method
- pathways method
- orthologs method
- genes method
- Bio::KEGG:REACTION#rpairs
- Bio::KEGG::ORTHOLOGY
- Bio::RestrictionEnzyme
- Known problems
-
RELEASE_NOTES-1.4.1
- BioRuby 1.4.1 RELEASE NOTES
- New features
- PAML Codeml support is significantly improved
- KEGG PATHWAY and KEGG MODULE parser
- Bio::KEGG improvements
- Test codes are added and improved.
- Other new methods
- Bug fixes
- Bio::Tree
- Bio::KEGG::GENES and Bio::KEGG::GENOME
- Other bug fixes
- Incompatible changes
- Bio::PAML::Codeml::Report
- Bio::KEGG::ORTHOLOGY
- Bio::AAindex2
- Bio::MEDLINE
- Known issues
- String escaping of command-line arguments in Ruby 1.9.X on Windows
-
RELEASE_NOTES-1.4.2
- BioRuby 1.4.2 RELEASE NOTES
- New features
- Speed-up of Bio::RestrictionEnzyme::Analysis.cut
- New classes Bio::DDBJ::REST, REST interface for DDBJ web service
- Bio::Blast with remote DDBJ server uses REST instead of SOAP
- Tutorial is updated
- Many unit tests are added
- Other new features
- Bug fixes
- Bio::Blast
- Bio::SPTR (Bio::UniProt)
- Other bug fixes
- Incompatible changes
- Bio::Sequence#output(:fastq)
- Bio::SPTR CC line topic “WEB RESOURCE”
- Bio::Blast with the remote GenomeNet server
- Bio::Blast with the remote DDBJ server
- Bio::RestrictionEnzyme internal data structure change
- Known issues
- Other important news
-
RELEASE_NOTES-1.4.3
- BioRuby 1.4.3 RELEASE NOTES
- New features
- Bio::KEGG::KGML
- Improvements
- Portability running on JRuby and Rubinius
- Testing on Travis CI
- Bug fixes
- Strange behavior related with “circular require” is fixed
- Other bug fixes
- Incompatible changes and removed features
- Bio::FlatFile use binmode (binary mode) when opening a file
- Broader FASTQ file recognition
- Bio::KEGG::KGML
- Bio::EMBL#os
- Tests
- Other removed features
- Known issues
- JRuby
- Rubinius
- DDBJ Web API related classes (Bio::DDBJ::*, Bio::BLAST::Remote::DDBJ)
- SOAP4R with Ruby 1.9
-
RELEASE_NOTES-1.5.0
- BioRuby 1.5.0 RELEASE NOTES
- NEWS
- Full support of Ruby 2.0.0, 2.1, and 2.2
- Support of Ruby 1.8 will be stopped
- License is updated to the new Ruby’s License
- Semantic Versioning will be introduced
- New features and improvements
- New method Bio::FastaFormat#first_name
- Accuracy of Bio::SiRNA
- Speed up of Bio::ClustalW::Report
- Many warning messages are squashed
- Refactoring of codes
- Bug fixes
- Bugs due to remote server changes
- Bio::PubMed
- Bio::Hinv
- Bio::TogoWS::REST
- Bio::Fetch
- BioSQL
- Bugs found in data format parsers
- Other bugs
- Renamed features
- Bio::SPTR, Bio::UniProt, Bio::SwissProt, and Bio::TrEMBL => Bio::UniProtKB
- Deprecated features
- Bio::RefSeq, Bio::DDBJ
- Removed features
- Bio::SOAPWSDL
- Bio::EBI::SOAP
- Bio::KEGG::API
- Bio::DBGET
- Bio::Ensembl
- Bio::DDBJ::XML, Bio::DDBJ::REST
- Bio::HGC::HiGet
- Bio::NCBI::SOAP
- Bio::KEGG::Taxonomy
- Bio.method_missing
- extconf.rb
- Incompatible changes
- Bio::Fetch
- Known issues
- Bio::PDB
- Bio::Blast::Report
- Bio::Blast::Default::Report
Classes and Modules
-
Bio
- bio.rb - Loading all BioRuby modules
- bio/appl/bl2seq/report.rb - bl2seq (BLAST 2 sequences) parser
- Acknowledgements
- bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser
- Note
- bio/appl/blast/remote.rb - remote BLAST wrapper basic module
- bio/appl/blast/wublast.rb - WU-BLAST default output parser
- Description
- References
- bio/appl/emboss.rb - EMBOSS wrapper
- bio/appl/gcg/seq.rb - GCG sequence file format class (.seq/.pep file)
- About Bio::GCG::Seq
- bio/appl/iprscan/report.rb - a class for iprscan output.
- Report classes for the iprscan program.
- bio/appl/meme/motif.rb - Class to represent a sequence motif
- Description
- References
- bio/appl/muscle.rb - MUSCLE application wrapper class
- References
- bio/appl/phylip/alignment.rb - phylip multiple alignment format parser
- About Bio::Phylip::PhylipFormat
- bio/appl/probcons.rb - ProbCons application wrapper class
- References
- bio/appl/sim4/report.rb - sim4 result parser
- References
- bio/appl/sosui/report.rb - SOSUI report class
- Example
- References
- bio/appl/targetp/report.rb - TargetP report class
- Description
- Example
- References
- bio/appl/tcoffee.rb - T-Coffee application wrapper class
- References
- bio/compat/references.rb - Obsoleted References class
- Description
- bio/data/aa.rb - Amino Acids
- bio/data/codontable.rb - Codon Table
- Data source
- Examples
- bio/data/na.rb - Nucleic Acids
- Synopsis
- Usage
- bio/db/fasta/defline.rb - FASTA defline parser class
- Description
- Examples
- References
- bio/db/kegg/common.rb - Common methods for KEGG database classes
- Description
- bio/db/kegg/genes.rb - KEGG/GENES database class
- KEGG GENES parser
- Examples
- bio/db/kegg/keggtab.rb - KEGG keggtab class
- bio/db/pdb/chain.rb - chain class for PDB
- Bio::PDB::Chain
- bio/db/pdb/chemicalcomponent.rb - PDB Chemical Component Dictionary parser
- About Bio::PDB::ChemicalComponent
- References
- bio/db/pdb/model.rb - model class for PDB
- Bio::PDB::Model
- bio/db/pdb/residue.rb - residue class for PDB
- Bio::PDB::Residue
- Bio::PDB::Heterogen
- bio/feature.rb - Features/Feature class (GenBank Feature table)
- bio/io/flatfile.rb - flatfile access wrapper class
- bio/location.rb - Locations/Location class (GenBank location format)
- bio/sequence.rb - biological sequence class
- bio/sequence/aa.rb - amino acid sequence class
- bio/sequence/adapter.rb - Bio::Sequence adapter helper module
- bio/sequence/common.rb - common methods for biological sequence
- bio/sequence/compat.rb - methods for backward compatibility
- bio/sequence/dblink.rb - sequence ID with database name
- bio/sequence/generic.rb - generic sequence class to store an intact string
- bio/sequence/na.rb - nucleic acid sequence class
- bio/sequence/quality_score.rb - Sequence quality score manipulation modules
- Description
- References
- bio/sequence/sequence_masker.rb - Sequence masking helper methods
- Description
- bio/tree/output.rb - Phylogenetic tree formatter
- Description
- References
- bio/version.rb - BioRuby version information
- Bio::AAindex
- Bio::AAindex1
- Bio::AAindex2
- Bio::Abif
- Bio::Abif::DirectoryEntry
-
Bio::Alignment
- About Bio::Alignment
- Multiple alignment container classes
- Bio::Alignment::OriginalAlignment
- Bio::Alignment::SequenceArray
- Bio::Alignment::SequenceHash
- Bio::Alignment::Site
- Modules
- Bio::Alignment::EnumerableExtension
- Bio::Alignment::ArrayExtension
- Bio::Alignment::HashExtension
- Bio::Alignment::SiteMethods
- Bio::Alignment::PropertyMethods
- Bio::Alignment::GAP
- Compatibility from older BioRuby
- Bio::Alignment::ArrayExtension
- Bio::Alignment::EnumerableExtension
- Bio::Alignment::FactoryTemplate
- Bio::Alignment::FactoryTemplate::FileInFileOut
- Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- Bio::Alignment::FactoryTemplate::FileInStdoutOut
- Bio::Alignment::FactoryTemplate::Simple
- Bio::Alignment::FactoryTemplate::StdinInFileOut
- Bio::Alignment::FactoryTemplate::WrapInputStdin
- Bio::Alignment::FactoryTemplate::WrapInputTempfile
- Bio::Alignment::FactoryTemplate::WrapOutputStdout
- Bio::Alignment::FactoryTemplate::WrapOutputTempfile
- Bio::Alignment::GAP
- Bio::Alignment::HashExtension
- Bio::Alignment::MultiFastaFormat
- Bio::Alignment::OriginalAlignment
- Bio::Alignment::OriginalPrivate
- Bio::Alignment::Output
- Bio::Alignment::PropertyMethods
- Bio::Alignment::SequenceArray
- Bio::Alignment::SequenceHash
- Bio::Alignment::Site
- Bio::Alignment::SiteMethods
- Bio::AminoAcid
- Bio::AminoAcid::Data
- Bio::Blast
- Bio::Blast::Bl2seq
- Bio::Blast::Bl2seq::Report
- Bio::Blast::Bl2seq::Report::HSP
- Bio::Blast::Bl2seq::Report::Hit
- Bio::Blast::Bl2seq::Report::Iteration
- Bio::Blast::Default
- Bio::Blast::Default::Report
- Bio::Blast::Default::Report::HSP
- Bio::Blast::Default::Report::Hit
- Bio::Blast::Default::Report::Iteration
- Bio::Blast::Default::Report_TBlast
- Bio::Blast::Fastacmd
- Bio::Blast::NCBIOptions
- Bio::Blast::RPSBlast
- Bio::Blast::RPSBlast::RPSBlastSplitter
- Bio::Blast::RPSBlast::Report
- Bio::Blast::RPSBlast::Report::FLATFILE_SPLITTER
- Bio::Blast::RPSBlast::Report::Iteration
- Bio::Blast::Remote
- Bio::Blast::Remote::GenomeNet
- Bio::Blast::Remote::GenomeNet::Information
- Bio::Blast::Remote::Genomenet
- Bio::Blast::Remote::Information
- Bio::Blast::Report
- Bio::Blast::Report::BlastXmlSplitter
- Bio::Blast::Report::FLATFILE_SPLITTER
- Bio::Blast::Report::Hit
- Bio::Blast::Report::Hsp
- Bio::Blast::Report::Iteration
- Bio::Blast::Report_tab
- Bio::Blast::WU
- Bio::Blast::WU::Report
- Bio::Blast::WU::Report::HSP
- Bio::Blast::WU::Report::Hit
- Bio::Blast::WU::Report::Iteration
- Bio::Blast::WU::Report_TBlast
- Bio::Blat
- Bio::Blat::Report
- Bio::Blat::Report::Hit
- Bio::Blat::Report::SegmentPair
- Bio::Blat::Report::SeqDesc
- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
- Bio::ColorScheme
- Bio::Command
- Bio::Command::Tmpdir
- Bio::Command::Tmpdir::Remover
- Bio::ContingencyTable
- Bio::DAS
- Bio::DAS::DNA
- Bio::DAS::DSN
- Bio::DAS::ENTRY_POINT
- Bio::DAS::FEATURE
- Bio::DAS::GFF
- Bio::DAS::GROUP
- Bio::DAS::LINK
- Bio::DAS::SEGMENT
- Bio::DAS::SEQUENCE
- Bio::DAS::TARGET
- Bio::DAS::TYPE
- Bio::DAS::TYPES
- Bio::DB
- Bio::DDBJ
- Bio::EMBL
- Bio::EMBLDB
- Bio::EMBLDB::Common
- Bio::EMBOSS
- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
- Bio::FANTOM::MaXML::Annotations
- Bio::FANTOM::MaXML::Cluster
- Bio::FANTOM::MaXML::Sequence
- Bio::FANTOM::MaXML::Sequences
- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
- Bio::Fasta::Report::Hit::Target
- Bio::Fasta::Report::Program
- Bio::FastaDefline
- Bio::FastaFormat
- Bio::FastaNumericFormat
- Bio::Fastq
- Bio::Fastq::Error
- Bio::Fastq::Error::Diff_ids
- Bio::Fastq::Error::Long_qual
- Bio::Fastq::Error::No_atmark
- Bio::Fastq::Error::No_ids
- Bio::Fastq::Error::No_qual
- Bio::Fastq::Error::No_seq
- Bio::Fastq::Error::Qual_char
- Bio::Fastq::Error::Qual_range
- Bio::Fastq::Error::Seq_char
- Bio::Fastq::Error::Short_qual
- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
- Bio::Fastq::FormatData::FASTQ_SANGER
- Bio::Fastq::FormatData::FASTQ_SOLEXA
- Bio::Feature
- Bio::Feature::Qualifier
- Bio::Features
- Bio::Fetch
- Bio::Fetch::EBI
- Bio::FlatFile
- Bio::FlatFile::AutoDetect
- Bio::FlatFile::AutoDetect::RuleDebug
- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
- Bio::FlatFile::AutoDetect::RuleTemplate
- Bio::FlatFile::AutoDetect::RulesArray
- Bio::FlatFile::BufferedInputStream
- Bio::FlatFile::Splitter
- Bio::FlatFile::Splitter::Default
- Bio::FlatFile::Splitter::LineOriented
- Bio::FlatFile::Splitter::Template
- Bio::FlatFile::UnknownDataFormatError
- Bio::FlatFileIndex
- Bio::FlatFileIndex::BDB_1
- Bio::FlatFileIndex::BDB_1::BDBMappingFile
- Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- Bio::FlatFileIndex::BDBdefault
- Bio::FlatFileIndex::BDBwrapper
- Bio::FlatFileIndex::DEBUG
- Bio::FlatFileIndex::DataBank
- Bio::FlatFileIndex::FileID
- Bio::FlatFileIndex::FileIDs
- Bio::FlatFileIndex::Flat_1
- Bio::FlatFileIndex::Flat_1::FlatMappingFile
- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- Bio::FlatFileIndex::Flat_1::Record
- Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- Bio::FlatFileIndex::Indexer
- Bio::FlatFileIndex::Indexer::NameSpace
- Bio::FlatFileIndex::Indexer::NameSpaces
- Bio::FlatFileIndex::Indexer::Parser
- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
- Bio::FlatFileIndex::Results
- Bio::FlatFileIndex::Template
- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
- Bio::GCG::Msf
- Bio::GCG::Seq
- Bio::GFF
- Bio::GFF::GFF2
- Bio::GFF::GFF2::Escape
- Bio::GFF::GFF2::MetaData
- Bio::GFF::GFF2::Record
- Bio::GFF::GFF2::Record::Value
- Bio::GFF::GFF3
- Bio::GFF::GFF3::Escape
- Bio::GFF::GFF3::Record
- Bio::GFF::GFF3::Record::Gap
- Bio::GFF::GFF3::Record::Gap::Code
- Bio::GFF::GFF3::Record::Target
- Bio::GFF::GFF3::RecordBoundary
- Bio::GFF::GFF3::SequenceRegion
- Bio::GFF::Record
- Bio::GO
- Bio::GO::External2go
- Bio::GO::GeneAssociation
- Bio::GO::Ontology
- Bio::GenBank
- Bio::GenBank::Locus
- Bio::GenPept
- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HMMER
- Bio::HMMER::Report
- Bio::HMMER::Report::Hit
- Bio::HMMER::Report::Hsp
- Bio::Hinv
- Bio::Hinv::Acc2hit
- Bio::Hinv::Common
- Bio::Hinv::Hit2acc
- Bio::Hinv::HitCnt
- Bio::Hinv::HitDefinition
- Bio::Hinv::HitPubmedId
- Bio::Hinv::HitXML
- Bio::Hinv::Hix2hit
- Bio::Hinv::HixCnt
- Bio::Hinv::HixRepresent
- Bio::Hinv::HixXML
- Bio::Hinv::IdSearch
- Bio::Hinv::KeywordSearch
- Bio::Iprscan
- Bio::Iprscan::Report
- Bio::Iprscan::Report::Match
- Bio::KEGG
- Bio::KEGG::BRITE
- Bio::KEGG::COMPOUND
- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::DiseasesAsHash
- Bio::KEGG::Common::GenesAsHash
- Bio::KEGG::Common::ModulesAsHash
- Bio::KEGG::Common::OrthologsAsHash
- Bio::KEGG::Common::PathwaysAsHash
- Bio::KEGG::Common::References
- Bio::KEGG::Common::StringsAsHash
- Bio::KEGG::DRUG
- Bio::KEGG::ENZYME
- Bio::KEGG::EXPRESSION
- Bio::KEGG::GENES
- Bio::KEGG::GENOME
- Bio::KEGG::GLYCAN
- Bio::KEGG::KGML
- Bio::KEGG::KGML::Entry
- Bio::KEGG::KGML::Graphics
- Bio::KEGG::KGML::Product
- Bio::KEGG::KGML::Reaction
- Bio::KEGG::KGML::Relation
- Bio::KEGG::KGML::Substrate
- Bio::KEGG::KGML::SubstrateProduct
- Bio::KEGG::Keggtab
- Bio::KEGG::Keggtab::DB
- Bio::KEGG::MODULE
- Bio::KEGG::ORTHOLOGY
- Bio::KEGG::PATHWAY
- Bio::KEGG::REACTION
- Bio::KEGGDB
- Bio::LITDB
- Bio::Lasergene
- Bio::Location
- Bio::Locations
- Bio::MAFFT
- Bio::MAFFT::Report
- Bio::MEDLINE
- Bio::Map
- Bio::Map::ActsLikeMap
- Bio::Map::ActsLikeMarker
- Bio::Map::Mapping
- Bio::Map::Marker
- Bio::Map::SimpleMap
- Bio::Meme
- Bio::Meme::Mast
- Bio::Meme::Mast::Report
- Bio::Meme::Motif
- Bio::Muscle
- Bio::Muscle::DEFAULT_PARSER
- Bio::NBRF
- Bio::NCBI
- Bio::NCBI::REST
- Bio::NCBI::REST::EFetch
- Bio::NCBI::REST::EFetch::Methods
- Bio::NCBI::REST::ESearch
- Bio::NCBI::REST::ESearch::Methods
- Bio::NCBIDB
- Bio::NCBIDB::Common
- Bio::Newick
- Bio::Newick::ParseError
- Bio::Nexus
- Bio::Nexus::CharactersBlock
- Bio::Nexus::DataBlock
- Bio::Nexus::DistancesBlock
- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
- Bio::Nexus::NexusMatrix::NexusMatrixError
- Bio::Nexus::NexusParseError
- Bio::Nexus::TaxaBlock
- Bio::Nexus::TreesBlock
- Bio::Nexus::Util
- Bio::NucleicAcid
- Bio::NucleicAcid::Data
- Bio::PAML
- Bio::PAML::Baseml
- Bio::PAML::Baseml::Report
- Bio::PAML::Codeml
- Bio::PAML::Codeml::Model
- Bio::PAML::Codeml::PositiveSite
- Bio::PAML::Codeml::PositiveSites
- Bio::PAML::Codeml::Rates
- Bio::PAML::Codeml::Report
- Bio::PAML::Codeml::ReportError
- Bio::PAML::Codeml::ReportSingle
- Bio::PAML::Common
- Bio::PAML::Common::Report
- Bio::PAML::Yn00
- Bio::PAML::Yn00::Report
- Bio::PDB
- Bio::PDB::AtomFinder
- Bio::PDB::Chain
- Bio::PDB::ChainFinder
- Bio::PDB::ChemicalComponent
- Bio::PDB::ChemicalComponent::Record
- Bio::PDB::Coordinate
- Bio::PDB::DataType
- Bio::PDB::DataType::ConstLikeMethod
- Bio::PDB::DataType::Pdb_AChar
- Bio::PDB::DataType::Pdb_Atom
- Bio::PDB::DataType::Pdb_Character
- Bio::PDB::DataType::Pdb_Date
- Bio::PDB::DataType::Pdb_IDcode
- Bio::PDB::DataType::Pdb_Integer
- Bio::PDB::DataType::Pdb_LString
- Bio::PDB::DataType::Pdb_List
- Bio::PDB::DataType::Pdb_Real
- Bio::PDB::DataType::Pdb_Residue_name
- Bio::PDB::DataType::Pdb_SList
- Bio::PDB::DataType::Pdb_Specification_list
- Bio::PDB::DataType::Pdb_String
- Bio::PDB::DataType::Pdb_StringRJ
- Bio::PDB::DataType::Pdb_SymOP
- Bio::PDB::HetatmFinder
- Bio::PDB::Heterogen
- Bio::PDB::HeterogenFinder
- Bio::PDB::Model
- Bio::PDB::ModelFinder
- Bio::PDB::Record
- Bio::PDB::Record::ANISOU
- Bio::PDB::Record::ATOM
- Bio::PDB::Record::HETATM
- Bio::PDB::Record::Jrnl
- Bio::PDB::Record::Remark1
- Bio::PDB::Record::Remark2
- Bio::PDB::Residue
- Bio::PDB::ResidueFinder
- Bio::PDB::Utils
- Bio::PROSITE
- Bio::PSORT
- Bio::PSORT::CGIDriver
- Bio::PSORT::IPSORT
- Bio::PSORT::PSORT1
- Bio::PSORT::PSORT1::Remote
- Bio::PSORT::PSORT1::Report
- Bio::PSORT::PSORT2
- Bio::PSORT::PSORT2::Remote
- Bio::PSORT::PSORT2::Report
- Bio::PSORT::PSORTB
- Bio::PSORT::WoLF_PSORT
- Bio::PTS1
- Bio::PTS1::Report
- Bio::Pathway
- Bio::Phylip
- Bio::Phylip::DistanceMatrix
- Bio::Phylip::PhylipFormat
- Bio::Probcons
- Bio::Probcons::DEFAULT_PARSER
- Bio::PubMed
- Bio::REBASE
- Bio::RefSeq
- Bio::Reference
- Bio::References
- Bio::Registry
- Bio::Registry::DB
- Bio::Relation
- Bio::RestrictionEnzyme
- Bio::RestrictionEnzyme::Analysis
- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- Bio::RestrictionEnzyme::DenseIntArray
- Bio::RestrictionEnzyme::DoubleStranded
- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction
- Bio::RestrictionEnzyme::Fragments
- Bio::RestrictionEnzyme::Range
- Bio::RestrictionEnzyme::Range::CutRange
- Bio::RestrictionEnzyme::Range::CutRanges
- Bio::RestrictionEnzyme::Range::HorizontalCutRange
- Bio::RestrictionEnzyme::Range::SequenceRange
- Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- Bio::RestrictionEnzyme::Range::VerticalCutRange
- Bio::RestrictionEnzyme::SingleStrand
- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::SingleStrandComplement
- Bio::RestrictionEnzyme::SortedNumArray
- Bio::RestrictionEnzyme::StringFormatting
- Bio::SOFT
- Bio::SOSUI
- Bio::SOSUI::Report
- Bio::SOSUI::Report::TMH
- Bio::SangerChromatogram
- Bio::Scf
- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::Adapter
- Bio::Sequence::Adapter::EMBL
- Bio::Sequence::Adapter::FastaFormat
- Bio::Sequence::Adapter::FastaNumericFormat
- Bio::Sequence::Adapter::Fastq
- Bio::Sequence::Adapter::GenBank
- Bio::Sequence::Adapter::SangerChromatogram
- Bio::Sequence::Common
- Bio::Sequence::DBLink
- Bio::Sequence::Format
- Bio::Sequence::Format::AminoFormatter
- Bio::Sequence::Format::Formatter
- Bio::Sequence::Format::Formatter::Fasta
- Bio::Sequence::Format::Formatter::Fasta_ncbi
- Bio::Sequence::Format::Formatter::Fasta_numeric
- Bio::Sequence::Format::Formatter::Fastq
- Bio::Sequence::Format::Formatter::Fastq_illumina
- Bio::Sequence::Format::Formatter::Fastq_sanger
- Bio::Sequence::Format::Formatter::Fastq_solexa
- Bio::Sequence::Format::Formatter::Qual
- Bio::Sequence::Format::Formatter::Raw
- Bio::Sequence::Format::FormatterBase
- Bio::Sequence::Format::INSDFeatureHelper
- Bio::Sequence::Format::NucFormatter
- Bio::Sequence::Format::NucFormatter::Embl
- Bio::Sequence::Format::NucFormatter::Genbank
- Bio::Sequence::NA
- Bio::Sequence::QualityScore
- Bio::Sequence::QualityScore::Converter
- Bio::Sequence::QualityScore::Phred
- Bio::Sequence::QualityScore::Solexa
- Bio::Sequence::SequenceMasker
- Bio::SiRNA
- Bio::SiRNA::Pair
- Bio::SiRNA::ShRNA
- Bio::Sim4
- Bio::Sim4::Report
- Bio::Sim4::Report::Hit
- Bio::Sim4::Report::Segment
- Bio::Sim4::Report::SegmentPair
- Bio::Sim4::Report::SeqDesc
- Bio::Spidey
- Bio::Spidey::Report
- Bio::Spidey::Report::Hit
- Bio::Spidey::Report::Segment
- Bio::Spidey::Report::SegmentPair
- Bio::Spidey::Report::SeqDesc
- Bio::SwissProt
- Bio::TMHMM
- Bio::TMHMM::Report
- Bio::TMHMM::TMH
- Bio::TRANSFAC
- Bio::TRANSFAC::CELL
- Bio::TRANSFAC::CLASS
- Bio::TRANSFAC::FACTOR
- Bio::TRANSFAC::GENE
- Bio::TRANSFAC::MATRIX
- Bio::TRANSFAC::SITE
- Bio::TargetP
- Bio::TargetP::Report
- Bio::Tcoffee
- Bio::Tcoffee::DEFAULT_PARSER
- Bio::TogoWS
- Bio::TogoWS::AccessWait
- Bio::TogoWS::REST
- Bio::TrEMBL
- Bio::Tree
- Bio::Tree::Edge
- Bio::Tree::NoPathError
- Bio::Tree::Node
- Bio::UniProt
- Bio::UniProtKB
- Object
Methods
- ::[] — Bio::CodonTable
- ::[] — Bio::PDB::Coordinate
- ::[] — Bio::FlatFile::AutoDetect
- ::[] — Bio::FlatFile::AutoDetect::RuleTemplate
- ::[] — Bio::RestrictionEnzyme::DenseIntArray
- ::[] — Bio::RestrictionEnzyme::SortedNumArray
- ::[] — Bio::PDB::DataType::Pdb_String
- ::[] — Bio::PDB::DataType::Pdb_LString
- ::[] — Bio::PDB::DataType::Pdb_Real
- ::[] — Bio::PDB::DataType::Pdb_String
- ::[] — Bio::PDB::DataType::Pdb_String
- ::[] — Bio::PDB::DataType::Pdb_String
- ::[] — Bio::PDB::DataType::Pdb_String
- ::[] — Bio::PDB::DataType::Pdb_String
- ::[] — Bio::PDB::DataType::Pdb_String
- ::[] — Bio::PDB::DataType::Pdb_LString
- ::acc2hit — Bio::Hinv
- ::acos — Bio::PDB::Utils
- ::adapter — Bio::Sequence
- ::addindex_bdb — Bio::FlatFileIndex::Indexer
- ::addindex_flat — Bio::FlatFileIndex::Indexer
- ::align — Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- ::align_with_cuts — Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- ::array_to_string — Bio::Nexus::Util
- ::auto — Bio::AAindex
- ::auto — Bio::FlatFile
- ::auto — Bio::Sequence
- ::autodetect — Bio::FlatFile
- ::autodetect_file — Bio::FlatFile
- ::autodetect_io — Bio::FlatFile
- ::autodetect_stream — Bio::FlatFile
- ::both_intron — Bio::Sim4::Report::SegmentPair
- ::calc_checksum — Bio::GCG::Seq
- ::calculatePlane — Bio::PDB::Utils
- ::chose_sort_proc — Bio::FlatFileIndex::Indexer
- ::continue? — Bio::PDB::Record
- ::convert — Bio::TogoWS::REST
- ::convert_to_xyz — Bio::PDB::Utils
- ::copy — Bio::CodonTable
- ::create — Bio::FlatFileIndex::Flat_1::Record
- ::create_config_file — Bio::PAML::Codeml
- ::create_control_file — Bio::PAML::Codeml
- ::create_definition_hash — Bio::PDB::Record
- ::cut — Bio::RestrictionEnzyme
- ::cut — Bio::RestrictionEnzyme::Analysis
- ::cut_symbol — Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- ::cut_symbol= — Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- ::cut_without_permutations — Bio::RestrictionEnzyme::Analysis
- ::def_rec — Bio::PDB::Record
- ::default — Bio::FlatFile::AutoDetect
- ::default= — Bio::FlatFile::AutoDetect
- ::default_email — Bio::NCBI
- ::default_email= — Bio::NCBI
- ::default_parser — Bio::PSORT::PSORT1::Report
- ::default_parser — Bio::PSORT::PSORT2::Report
- ::default_tool — Bio::NCBI
- ::default_tool= — Bio::NCBI
- ::dihedral_angle — Bio::PDB::Utils
- ::distance — Bio::PDB::Utils
- ::divent — Bio::PSORT::PSORT2::Report
- ::efetch — Bio::NCBI::REST
- ::efetch — Bio::PubMed
- ::einfo — Bio::NCBI::REST
- ::elements — Bio::PDB::Coordinate
- ::entret — Bio::EMBOSS
- ::entry — Bio::TogoWS::REST
- ::entry_database_list — Bio::TogoWS::REST
- ::enzyme_name? — Bio::RestrictionEnzyme
- ::escaped_cut_symbol — Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- ::esearch — Bio::NCBI::REST
- ::esearch — Bio::PubMed
- ::esearch_count — Bio::NCBI::REST
- ::external_merge_proc — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- ::external_merge_sort_proc — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- ::external_sort_proc — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- ::extract_key — Bio::Alignment::OriginalPrivate
- ::extract_seq — Bio::Alignment::OriginalPrivate
- ::fftns — Bio::MAFFT
- ::fftnsi — Bio::MAFFT
- ::filename — Bio::FlatFileIndex::DataBank
- ::flag_append — Bio::FlatFileIndex::BDBdefault
- ::flag_read — Bio::FlatFileIndex::BDBdefault
- ::flag_write — Bio::FlatFileIndex::BDBdefault
- ::for_io — Bio::FlatFile::BufferedInputStream
- ::foreach — Bio::FlatFile
- ::formatstring2class — Bio::FlatFileIndex
- ::gapped_pos — Bio::Alignment::GAP
- ::generate — Bio::Phylip::DistanceMatrix
- ::genomenet — Bio::Blast::Remote
- ::get_by_id — Bio::FANTOM
- ::get_record_class — Bio::PDB::ChemicalComponent::Record
- ::get_record_class — Bio::PDB::Record
- ::get_residue_id_from_atom — Bio::PDB::Residue
- ::guess — Bio::Sequence
- ::hit2acc — Bio::Hinv
- ::hit_cnt — Bio::Hinv
- ::hit_definition — Bio::Hinv
- ::hit_pubmedid — Bio::Hinv
- ::hit_xml — Bio::Hinv
- ::hix2hit — Bio::Hinv
- ::hix_cnt — Bio::Hinv
- ::hix_represent — Bio::Hinv
- ::id_search — Bio::Hinv
- ::imsut — Bio::PSORT::PSORT1
- ::imsut — Bio::PSORT::PSORT2
- ::input — Bio::Sequence
- ::internal_sort_proc — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- ::keyword_search — Bio::Hinv
- ::larger_than_zero — Bio::Nexus::Util
- ::load_yaml — Bio::REBASE
- ::local — Bio::Blast
- ::local — Bio::Fasta
- ::longer_than_zero — Bio::Nexus::Util
- ::make_default — Bio::FlatFile::AutoDetect
- ::makeindex — Bio::FlatFileIndex
- ::makeindexBDB — Bio::FlatFileIndex::Indexer
- ::makeindexFlat — Bio::FlatFileIndex::Indexer
- ::new — Bio::Alignment::OriginalAlignment
- ::new — Bio::Alignment::FactoryTemplate::Simple
- ::new — Bio::Blast
- ::new — Bio::Blast::Bl2seq::Report::Iteration
- ::new — Bio::Blast::Default::Report
- ::new — Bio::Blast::Default::Report::Iteration
- ::new — Bio::Blast::Default::Report::Hit
- ::new — Bio::Blast::Default::Report::HSP
- ::new — Bio::Blast::Report
- ::new — Bio::Blast::NCBIOptions
- ::new — Bio::Blast::Report::Iteration
- ::new — Bio::Blast::Report::Hit
- ::new — Bio::Blast::Report::Hsp
- ::new — Bio::Blast::Report::BlastXmlSplitter
- ::new — Bio::Blast::Report::BlastXmlSplitter
- ::new — Bio::Blast::RPSBlast::RPSBlastSplitter
- ::new — Bio::Blast::RPSBlast::Report
- ::new — Bio::Blast::RPSBlast::RPSBlastSplitter
- ::new — Bio::Blast::RPSBlast::Report::Iteration
- ::new — Bio::Blast::WU::Report::Iteration
- ::new — Bio::Blast::WU::Report::Hit
- ::new — Bio::Blat::Report
- ::new — Bio::Blat::Report::SeqDesc
- ::new — Bio::Blat::Report::SegmentPair
- ::new — Bio::Blat::Report::Hit
- ::new — Bio::ClustalW
- ::new — Bio::ClustalW::Report
- ::new — Bio::EMBOSS
- ::new — Bio::Fasta
- ::new — Bio::Fasta::Report
- ::new — Bio::Fasta::Report::FastaFormat10Splitter
- ::new — Bio::Fasta::Report::FastaFormat10Splitter
- ::new — Bio::Fasta::Report::Program
- ::new — Bio::Fasta::Report::Hit
- ::new — Bio::Fasta::Report::Hit::Query
- ::new — Bio::GCG::Msf
- ::new — Bio::GCG::Seq
- ::new — Bio::Genscan::Report
- ::new — Bio::Genscan::Report::Gene
- ::new — Bio::Genscan::Report::Exon
- ::new — Bio::HMMER
- ::new — Bio::HMMER::Report
- ::new — Bio::HMMER::Report::Hit
- ::new — Bio::HMMER::Report::Hsp
- ::new — Bio::Iprscan::Report
- ::new — Bio::Iprscan::Report::Match
- ::new — Bio::MAFFT
- ::new — Bio::Alignment::MultiFastaFormat
- ::new — Bio::MAFFT::Report
- ::new — Bio::Meme::Mast
- ::new — Bio::Meme::Mast::Report
- ::new — Bio::Meme::Motif
- ::new — Bio::Alignment::MultiFastaFormat
- ::new — Bio::PAML::Codeml::Rates
- ::new — Bio::PAML::Codeml::Report
- ::new — Bio::PAML::Codeml::ReportSingle
- ::new — Bio::PAML::Codeml::Model
- ::new — Bio::PAML::Codeml::PositiveSite
- ::new — Bio::PAML::Codeml::PositiveSites
- ::new — Bio::PAML::Common
- ::new — Bio::PAML::Common::Report
- ::new — Bio::Phylip::PhylipFormat
- ::new — Bio::Phylip::DistanceMatrix
- ::new — Bio::Alignment::MultiFastaFormat
- ::new — Bio::PSORT::CGIDriver
- ::new — Bio::PSORT::PSORT1
- ::new — Bio::PSORT::PSORT1::Remote
- ::new — Bio::PSORT::PSORT2
- ::new — Bio::PSORT::PSORT2::Remote
- ::new — Bio::PSORT::PSORT1::Report
- ::new — Bio::PSORT::PSORT2::Report
- ::new — Bio::PTS1
- ::new — Bio::PTS1::Report
- ::new — Bio::Sim4
- ::new — Bio::Sim4::Report
- ::new — Bio::Sim4::Report::SeqDesc
- ::new — Bio::Sim4::Report::SegmentPair
- ::new — Bio::Sim4::Report::Segment
- ::new — Bio::Sim4::Report::Hit
- ::new — Bio::SOSUI::Report
- ::new — Bio::SOSUI::Report::TMH
- ::new — Bio::Spidey::Report
- ::new — Bio::Spidey::Report::SeqDesc
- ::new — Bio::Spidey::Report::SegmentPair
- ::new — Bio::Spidey::Report::Segment
- ::new — Bio::Spidey::Report::Hit
- ::new — Bio::TargetP::Report
- ::new — Bio::ClustalW::Report
- ::new — Bio::TMHMM::Report
- ::new — Bio::TMHMM::TMH
- ::new — Bio::Command::Tmpdir
- ::new — Bio::Command::Tmpdir::Remover
- ::new — Bio::Features
- ::new — Bio::Features
- ::new — Bio::References
- ::new — Bio::References
- ::new — Bio::CodonTable
- ::new — Bio::NCBIDB
- ::new — Bio::EMBLDB
- ::new — Bio::AAindex
- ::new — Bio::AAindex1
- ::new — Bio::AAindex2
- ::new — Bio::SwissProt
- ::new — Bio::TrEMBL
- ::new — Bio::FANTOM::MaXML
- ::new — Bio::FANTOM::MaXML::Annotation::DataSrc
- ::new — Bio::FastaFormat
- ::new — Bio::FastaDefline
- ::new — Bio::Sequence::Format::Formatter::Fasta
- ::new — Bio::Sequence::Format::Formatter::Fasta_numeric
- ::new — Bio::Sequence::Format::Formatter::Qual
- ::new — Bio::Fastq
- ::new — Bio::Fastq::FormatData
- ::new — Bio::Fastq::Error
- ::new — Bio::Sequence::Format::Formatter::Fastq
- ::new — Bio::Sequence::Format::Formatter::Fastq
- ::new — Bio::DDBJ
- ::new — Bio::GenBank::Locus
- ::new — Bio::GenPept::Locus
- ::new — Bio::RefSeq
- ::new — Bio::GFF
- ::new — Bio::GFF::Record
- ::new — Bio::GFF::GFF2
- ::new — Bio::GFF::GFF2::Record
- ::new — Bio::GFF::GFF2::Record::Value
- ::new — Bio::GFF::GFF2::MetaData
- ::new — Bio::GFF::GFF3
- ::new — Bio::GFF::GFF3::SequenceRegion
- ::new — Bio::GFF::GFF3::Record
- ::new — Bio::GFF::GFF3::Record::Target
- ::new — Bio::GFF::GFF3::Record::Gap
- ::new — Bio::GFF::GFF3::RecordBoundary
- ::new — Bio::GO::Ontology
- ::new — Bio::GO::GeneAssociation
- ::new — Bio::GO::External2go
- ::new — Bio::KEGG::BRITE
- ::new — Bio::KEGG::COMPOUND
- ::new — Bio::KEGG::DRUG
- ::new — Bio::KEGG::ENZYME
- ::new — Bio::KEGG::EXPRESSION
- ::new — Bio::KEGG::GENES
- ::new — Bio::KEGG::GENOME
- ::new — Bio::KEGG::GLYCAN
- ::new — Bio::KEGG::Keggtab
- ::new — Bio::KEGG::Keggtab::DB
- ::new — Bio::KEGG::KGML
- ::new — Bio::KEGG::KGML::SubstrateProduct
- ::new — Bio::KEGG::MODULE
- ::new — Bio::KEGG::ORTHOLOGY
- ::new — Bio::KEGG::PATHWAY
- ::new — Bio::KEGG::REACTION
- ::new — Bio::Lasergene
- ::new — Bio::LITDB
- ::new — Bio::MEDLINE
- ::new — Bio::NBRF
- ::new — Bio::Newick
- ::new — Bio::Nexus
- ::new — Bio::Nexus::GenericBlock
- ::new — Bio::Nexus::TaxaBlock
- ::new — Bio::Nexus::CharactersBlock
- ::new — Bio::Nexus::DataBlock
- ::new — Bio::Nexus::DistancesBlock
- ::new — Bio::Nexus::TreesBlock
- ::new — Bio::Nexus::NexusMatrix
- ::new — Bio::PDB
- ::new — Bio::PDB::Chain
- ::new — Bio::PDB::ChemicalComponent
- ::new — Bio::PDB::Model
- ::new — Bio::PDB::Residue
- ::new — Bio::PROSITE
- ::new — Bio::REBASE
- ::new — Bio::Abif
- ::new — Bio::Scf
- ::new — Bio::SOFT
- ::new — Bio::TRANSFAC
- ::new — Bio::TRANSFAC::MATRIX
- ::new — Bio::TRANSFAC::SITE
- ::new — Bio::TRANSFAC::FACTOR
- ::new — Bio::TRANSFAC::CELL
- ::new — Bio::TRANSFAC::CLASS
- ::new — Bio::TRANSFAC::GENE
- ::new — Bio::Feature
- ::new — Bio::Feature::Qualifier
- ::new — Bio::DAS
- ::new — Bio::DAS::ENTRY_POINT
- ::new — Bio::DAS::SEGMENT
- ::new — Bio::DAS::GFF
- ::new — Bio::DAS::FEATURE
- ::new — Bio::DAS::GROUP
- ::new — Bio::Blast::Fastacmd
- ::new — Bio::Fetch
- ::new — Bio::Fetch::EBI
- ::new — Bio::FlatFile
- ::new — Bio::FlatFile::AutoDetect
- ::new — Bio::FlatFile::AutoDetect::RuleTemplate
- ::new — Bio::FlatFile::AutoDetect::RuleDebug
- ::new — Bio::FlatFile::AutoDetect::RuleSpecial
- ::new — Bio::FlatFile::AutoDetect::RuleRegexp
- ::new — Bio::FlatFile::AutoDetect::RuleRegexp2
- ::new — Bio::FlatFile::AutoDetect::RuleProc
- ::new — Bio::FlatFileIndex
- ::new — Bio::FlatFileIndex::BDBwrapper
- ::new — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- ::new — Bio::FlatFile::BufferedInputStream
- ::new — Bio::FlatFileIndex::Template::NameSpace
- ::new — Bio::FlatFileIndex::FileID
- ::new — Bio::FlatFileIndex::FileIDs
- ::new — Bio::FlatFileIndex::Flat_1::Record
- ::new — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- ::new — Bio::FlatFileIndex::NameSpaces
- ::new — Bio::FlatFileIndex::DataBank
- ::new — Bio::FlatFileIndex::Indexer::NameSpace
- ::new — Bio::FlatFileIndex::Indexer::NameSpaces
- ::new — Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- ::new — Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- ::new — Bio::FlatFile::Splitter::Template
- ::new — Bio::FlatFile::Splitter::Default
- ::new — Bio::FlatFile::Splitter::LineOriented
- ::new — Bio::Hinv::Acc2hit
- ::new — Bio::Hinv::Hit2acc
- ::new — Bio::Hinv::HitCnt
- ::new — Bio::Hinv::HitDefinition
- ::new — Bio::Hinv::HitPubmedId
- ::new — Bio::Hinv::HitXML
- ::new — Bio::Hinv::Hix2hit
- ::new — Bio::Hinv::HixCnt
- ::new — Bio::Hinv::HixRepresent
- ::new — Bio::Hinv::KeywordSearch
- ::new — Bio::Hinv::IdSearch
- ::new — Bio::Registry
- ::new — Bio::Registry::DB
- ::new — Bio::TogoWS::REST
- ::new — Bio::Location
- ::new — Bio::Locations
- ::new — Bio::Map::Mapping
- ::new — Bio::Map::SimpleMap
- ::new — Bio::Map::Marker
- ::new — Bio::Pathway
- ::new — Bio::Relation
- ::new — Bio::Reference
- ::new — Bio::Sequence
- ::new — Bio::Sequence::AA
- ::new — Bio::Sequence::NA
- ::new — Bio::Sequence::DBLink
- ::new — Bio::Sequence::Format::FormatterBase
- ::new — Bio::Tree
- ::new — Bio::Tree::Edge
- ::new — Bio::Tree::Node
- ::new — Bio::ContingencyTable
- ::new — Bio::RestrictionEnzyme
- ::new — Bio::RestrictionEnzyme::DenseIntArray
- ::new — Bio::RestrictionEnzyme::DoubleStranded
- ::new — Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- ::new — Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- ::new — Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- ::new — Bio::RestrictionEnzyme::Range::HorizontalCutRange
- ::new — Bio::RestrictionEnzyme::Range::SequenceRange
- ::new — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- ::new — Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- ::new — Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- ::new — Bio::RestrictionEnzyme::Range::VerticalCutRange
- ::new — Bio::RestrictionEnzyme::SingleStrand
- ::new — Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- ::new — Bio::RestrictionEnzyme::SortedNumArray
- ::new — Bio::SiRNA
- ::new — Bio::SiRNA::Pair
- ::new — Bio::SiRNA::ShRNA
- ::new — Bio::Alignment
- ::new — Bio::Blast::Remote::GenomeNet
- ::new — Bio::Blast::Remote::GenomeNet
- ::new — Bio::EMBLDB::Common
- ::new — Bio::NCBIDB::Common
- ::new — Bio::PDB::DataType::Pdb_Integer
- ::new — Bio::PDB::DataType::Pdb_SList
- ::new — Bio::PDB::DataType::Pdb_List
- ::new — Bio::PDB::DataType::Pdb_Specification_list
- ::new — Bio::PDB::DataType::Pdb_String
- ::new — Bio::PDB::DataType::Pdb_LString
- ::new — Bio::PDB::DataType::Pdb_Real
- ::new — Bio::PDB::DataType::Pdb_StringRJ
- ::new — Bio::PDB::DataType::Pdb_String
- ::new — Bio::PDB::DataType::Pdb_String
- ::new — Bio::PDB::DataType::Pdb_String
- ::new — Bio::PDB::DataType::Pdb_String
- ::new — Bio::PDB::DataType::Pdb_String
- ::new — Bio::PDB::DataType::Pdb_String
- ::new — Bio::PDB::DataType::Pdb_LString
- ::new — Bio::FlatFileIndex::Indexer::Parser
- ::new2 — Bio::Alignment::OriginalAlignment
- ::new2 — Bio::MAFFT
- ::new2 — Bio::Alignment
- ::new_direct — Bio::PDB::Record
- ::new_from_sequences_na — Bio::GFF::GFF3::Record::Gap
- ::new_from_sequences_na_aa — Bio::GFF::GFF3::Record::Gap
- ::new_from_string — Bio::FlatFileIndex::FileID
- ::new_inherit — Bio::PDB::Record
- ::new_intron — Bio::Spidey::Report::SegmentPair
- ::new_with_fungi_function — Bio::PTS1
- ::new_with_general_function — Bio::PTS1
- ::new_with_metazoa_function — Bio::PTS1
- ::nwap — Bio::MAFFT
- ::nwns — Bio::MAFFT
- ::nwnsi — Bio::MAFFT
- ::okazaki — Bio::PSORT::PSORT1
- ::okazaki — Bio::PSORT::PSORT2
- ::open — Bio::Blast::Default::Report
- ::open — Bio::DB
- ::open — Bio::SangerChromatogram
- ::open — Bio::FlatFile
- ::open — Bio::FlatFileIndex
- ::open — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- ::open — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- ::open — Bio::FlatFileIndex::DataBank
- ::open_file — Bio::FlatFile
- ::open_file — Bio::FlatFile::BufferedInputStream
- ::open_uri — Bio::FlatFile
- ::open_uri — Bio::FlatFile::BufferedInputStream
- ::out — Bio::FlatFileIndex::DEBUG
- ::out= — Bio::FlatFileIndex::DEBUG
- ::output — Bio::Sequence::Format::FormatterBase
- ::p2q — Bio::Sequence::QualityScore::Phred
- ::p2q — Bio::Sequence::QualityScore::Solexa
- ::pa2re — Bio::PROSITE
- ::parse — Bio::Blast::NCBIOptions
- ::parse — Bio::Sim4::Report::SeqDesc
- ::parse — Bio::Sim4::Report::SegmentPair
- ::parse — Bio::Spidey::Report::SeqDesc
- ::parse — Bio::Spidey::Report::SegmentPair
- ::parse — Bio::GFF::GFF2::Record
- ::parse — Bio::GFF::GFF2::MetaData
- ::parse — Bio::GFF::GFF3::SequenceRegion
- ::parse — Bio::GFF::GFF3::Record
- ::parse — Bio::GFF::GFF3::Record::Target
- ::parse — Bio::GFF::GFF3::Record::Gap
- ::parse_embl_DR_line — Bio::Sequence::DBLink
- ::parse_goids — Bio::GO::Ontology
- ::parse_ptxt — Bio::Iprscan::Report
- ::parse_ptxt_entry — Bio::Iprscan::Report
- ::parse_raw — Bio::Iprscan::Report
- ::parse_raw_entry — Bio::Iprscan::Report
- ::parse_txt — Bio::Iprscan::Report
- ::parse_txt_entry — Bio::Iprscan::Report
- ::parse_uniprot_DR_line — Bio::Sequence::DBLink
- ::parser — Bio::Fasta
- ::parser — Bio::Genscan::Report::Exon
- ::parser — Bio::PSORT::PSORT1::Report
- ::parser — Bio::PSORT::PSORT2::Report
- ::parser — Bio::GO::GeneAssociation
- ::parser — Bio::GO::External2go
- ::peking — Bio::PSORT::PSORT1
- ::peking — Bio::PSORT::PSORT2
- ::permission — Bio::FlatFileIndex::BDBdefault
- ::pmfetch — Bio::PubMed
- ::print — Bio::FlatFileIndex::DEBUG
- ::q2p — Bio::Sequence::QualityScore::Phred
- ::q2p — Bio::Sequence::QualityScore::Solexa
- ::query — Bio::Fetch::EBI
- ::query — Bio::PubMed
- ::query — Bio::FANTOM
- ::rad2deg — Bio::PDB::Utils
- ::randomize — Bio::Sequence::AA
- ::randomize — Bio::Sequence::NA
- ::read — Bio::REBASE
- ::read — Bio::FlatFileIndex::DataBank
- ::read — Bio::Sequence
- ::readfiles — Bio::Alignment::OriginalAlignment
- ::readfiles — Bio::Alignment
- ::rebase — Bio::RestrictionEnzyme
- ::region — Bio::DAS::SEGMENT
- ::remote — Bio::Blast
- ::remote — Bio::Fasta
- ::remote — Bio::PSORT::PSORT2
- ::reports — Bio::Blast
- ::reports — Bio::HMMER
- ::reports — Bio::TMHMM
- ::reports_xml — Bio::Blast
- ::reset_entrez_default_parameters — Bio::NCBI
- ::retrieve — Bio::TogoWS::REST
- ::rexml — Bio::Blast::Report
- ::run — Bio::EMBOSS
- ::search — Bio::PubMed
- ::search — Bio::TogoWS::REST
- ::search_database_list — Bio::TogoWS::REST
- ::seq1_intron — Bio::Sim4::Report::SegmentPair
- ::seq2_intron — Bio::Sim4::Report::SegmentPair
- ::seqret — Bio::EMBOSS
- ::set_kNN_prob — Bio::PSORT::PSORT2::Report
- ::symbols — Bio::PDB::Record
- ::tab — Bio::Blast::Report
- ::to_a — Bio::FlatFile
- ::to_gcg — Bio::GCG::Seq
- ::to_nbrf — Bio::NBRF
- ::to_nexus_helper — Bio::Nexus::Util
- ::to_string — Bio::FlatFileIndex::Flat_1::Record
- ::to_xyz — Bio::PDB::Utils
- ::too_short_parser — Bio::PSORT::PSORT2::Report
- ::ungapped_pos — Bio::Alignment::GAP
- ::update_index — Bio::FlatFileIndex
- ::update_index — Bio::FlatFileIndex::Indexer
- ::v_parser — Bio::PSORT::PSORT2::Report
- ::validate_input — Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- #* — Bio::FlatFileIndex::Results
- #+ — Bio::FlatFileIndex::Results
- #+ — Bio::RestrictionEnzyme::DenseIntArray
- #+ — Bio::RestrictionEnzyme::SortedNumArray
- #+ — Bio::Sequence::Common
- #<< — Bio::Alignment::OriginalAlignment
- #<< — Bio::FlatFileIndex::Indexer::NameSpaces
- #<< — Bio::RestrictionEnzyme::DenseIntArray
- #<< — Bio::RestrictionEnzyme::SortedNumArray
- #<< — Bio::Sequence::Common
- #<=> — Bio::PDB::Chain
- #<=> — Bio::PDB::Model
- #<=> — Bio::PDB::Record::ATOM
- #<=> — Bio::PDB::Residue
- #<=> — Bio::Location
- #<=> — Bio::Map::Mapping
- #<=> — Bio::Relation
- #== — Bio::Alignment::OriginalAlignment
- #== — Bio::Blast::NCBIOptions
- #== — Bio::GFF::GFF2::Record
- #== — Bio::GFF::GFF2::Record::Value
- #== — Bio::GFF::GFF2::MetaData
- #== — Bio::GFF::GFF3::SequenceRegion
- #== — Bio::GFF::GFF3::Record::Target
- #== — Bio::GFF::GFF3::Record::Gap
- #== — Bio::FlatFileIndex::Flat_1::Record
- #== — Bio::Location
- #== — Bio::Locations
- #== — Bio::Reference
- #== — Bio::RestrictionEnzyme::DenseIntArray
- #== — Bio::RestrictionEnzyme::SortedNumArray
- #=== — Bio::Relation
- #Pdb_LString — Bio::PDB::DataType::ConstLikeMethod
- #Pdb_Real — Bio::PDB::DataType::ConstLikeMethod
- #Pdb_String — Bio::PDB::DataType::ConstLikeMethod
- #[] — Bio::Alignment::OriginalAlignment
- #[] — Bio::Features
- #[] — Bio::CodonTable
- #[] — Bio::AAindex2
- #[] — Bio::FANTOM::MaXML::Sequences
- #[] — Bio::FANTOM::MaXML::Annotations
- #[] — Bio::FastaNumericFormat
- #[] — Bio::PDB
- #[] — Bio::PDB::Chain
- #[] — Bio::PDB::Model
- #[] — Bio::PDB::Residue
- #[] — Bio::Feature
- #[] — Bio::FlatFileIndex::BDBwrapper
- #[] — Bio::FlatFileIndex::FileIDs
- #[] — Bio::Locations
- #[] — Bio::RestrictionEnzyme::DenseIntArray
- #[] — Bio::RestrictionEnzyme::SortedNumArray
- #[] — Bio::AminoAcid::Data
- #[] — Bio::NucleicAcid::Data
- #[]= — Bio::CodonTable
- #[]= — Bio::FlatFileIndex::BDBwrapper
- #[]= — Bio::FlatFileIndex::FileIDs
- #[]= — Bio::Registry::DB
- #[]= — Bio::RestrictionEnzyme::DenseIntArray
- #[]= — Bio::RestrictionEnzyme::SortedNumArray
- #__output_phylip_common — Bio::Alignment::Output
- #__store__ — Bio::Alignment::OriginalAlignment
- #aa — Bio::Sequence
- #aa — Bio::AminoAcid::Data
- #aalen — Bio::UniProtKB
- #aalen — Bio::UniProtKB
- #aalen — Bio::FastaFormat
- #aalen — Bio::GenPept
- #aalen — Bio::KEGG::GENES
- #aalen — Bio::NBRF
- #aaseq — Bio::GCG::Seq
- #aaseq — Bio::UniProtKB
- #aaseq — Bio::UniProtKB
- #aaseq — Bio::FastaFormat
- #aaseq — Bio::GenPept
- #aaseq — Bio::KEGG::GENES
- #aaseq — Bio::NBRF
- #aaseq — Bio::PDB::Chain
- #ab — Bio::MEDLINE
- #absolute — Bio::Locations
- #abstract — Bio::MEDLINE
- #ac — Bio::PROSITE
- #ac — Bio::TRANSFAC
- #ac — Bio::EMBLDB::Common
- #acc_version — Bio::FastaFormat
- #acc_version — Bio::FastaDefline
- #acc_version — Bio::NCBIDB::Common
- #acceptor_score — Bio::Genscan::Report::Exon
- #accession — Bio::Iprscan::Report::Match
- #accession — Bio::FastaFormat
- #accession — Bio::FastaDefline
- #accession — Bio::PDB
- #accession — Bio::EMBLDB::Common
- #accession — Bio::NCBIDB::Common
- #accessions — Bio::FastaFormat
- #accessions — Bio::FastaDefline
- #accessions — Bio::Sequence
- #accessions — Bio::EMBLDB::Common
- #accessions — Bio::NCBIDB::Common
- #activity — Bio::KEGG::DRUG
- #ad — Bio::MEDLINE
- #add — Bio::FlatFile::AutoDetect
- #add — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #add — Bio::FlatFileIndex::FileIDs
- #add — Bio::FlatFileIndex::Indexer::NameSpaces
- #addAtom — Bio::PDB::Residue
- #addChain — Bio::PDB::Model
- #addLigand — Bio::PDB::Chain
- #addModel — Bio::PDB
- #addResidue — Bio::PDB::Chain
- #addSolvent — Bio::PDB::Model
- #add_attribute — Bio::GFF::GFF2::Record
- #add_continuation — Bio::PDB::Record
- #add_cut_range — Bio::RestrictionEnzyme::Range::SequenceRange
- #add_cut_ranges — Bio::RestrictionEnzyme::Range::SequenceRange
- #add_cuts_from_cut_ranges — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #add_defline — Bio::FastaDefline
- #add_edge — Bio::Tree
- #add_exclusive — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #add_header_line — Bio::Blat::Report
- #add_header_line — Bio::Fastq
- #add_horizontal_cut_range — Bio::RestrictionEnzyme::Range::SequenceRange
- #add_line — Bio::Blat::Report
- #add_line — Bio::Fastq
- #add_mapping_as_map — Bio::Map::ActsLikeMap
- #add_mapping_as_marker — Bio::Map::ActsLikeMarker
- #add_node — Bio::Tree
- #add_nr — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #add_options — Bio::Blast::NCBIOptions
- #add_overwrite — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #add_record — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #add_secondary_namespaces — Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- #add_seq — Bio::Alignment::OriginalAlignment
- #add_sequences — Bio::Alignment::OriginalAlignment
- #add_spacing — Bio::RestrictionEnzyme::StringFormatting
- #add_taxon — Bio::Nexus::TaxaBlock
- #add_taxon — Bio::Nexus::DataBlock
- #add_token — Bio::Nexus::GenericBlock
- #add_tree — Bio::Nexus::TreesBlock
- #add_tree_name — Bio::Nexus::TreesBlock
- #adjacency_matrix — Bio::Tree
- #adjacent_nodes — Bio::Tree
- #affiliations — Bio::MEDLINE
- #alias_list — Bio::KEGG::Keggtab
- #aliases — Bio::KEGG::Keggtab
- #align — Bio::ClustalW::Report
- #align — Bio::MAFFT::Report
- #align — Bio::Sim4::Report::Hit
- #align — Bio::Spidey::Report::Hit
- #align — Bio::ClustalW::Report
- #align_len — Bio::Blat::Report::SegmentPair
- #align_len — Bio::Sim4::Report::SegmentPair
- #aligned_strands — Bio::RestrictionEnzyme::DoubleStranded
- #aligned_strands_with_cuts — Bio::RestrictionEnzyme::DoubleStranded
- #alignment — Bio::ClustalW::Report
- #alignment — Bio::GCG::Msf
- #alignment — Bio::Alignment::MultiFastaFormat
- #alignment — Bio::MAFFT::Report
- #alignment — Bio::Alignment::MultiFastaFormat
- #alignment — Bio::Phylip::PhylipFormat
- #alignment — Bio::Alignment::MultiFastaFormat
- #alignment — Bio::ClustalW::Report
- #alignment_collect — Bio::Alignment::OriginalAlignment
- #alignment_collect — Bio::Alignment::EnumerableExtension
- #alignment_collect — Bio::Alignment::HashExtension
- #alignment_concat — Bio::Alignment::EnumerableExtension
- #alignment_concat — Bio::Alignment::HashExtension
- #alignment_length — Bio::Alignment::EnumerableExtension
- #alignment_lstrip! — Bio::Alignment::EnumerableExtension
- #alignment_normalize! — Bio::Alignment::EnumerableExtension
- #alignment_rstrip! — Bio::Alignment::EnumerableExtension
- #alignment_site — Bio::Alignment::EnumerableExtension
- #alignment_slice — Bio::Alignment::EnumerableExtension
- #alignment_strip! — Bio::Alignment::EnumerableExtension
- #alignment_subseq — Bio::Alignment::EnumerableExtension
- #alignment_window — Bio::Alignment::EnumerableExtension
- #all_reac — Bio::KEGG::ENZYME
- #alpha — Bio::PAML::Codeml::Model
- #altid — Bio::FANTOM::MaXML::Sequence
- #always_check= — Bio::FlatFileIndex::DataBank
- #always_check_consistency — Bio::FlatFileIndex
- #always_check_consistency= — Bio::FlatFileIndex
- #ancestors — Bio::Tree
- #annotations — Bio::FANTOM::MaXML::Sequence
- #append — Bio::Features
- #append — Bio::References
- #append — Bio::Feature
- #append — Bio::Pathway
- #append_hsp — Bio::HMMER::Report::Hit
- #assoc — Bio::Feature
- #at_content — Bio::Sequence::NA
- #at_skew — Bio::Sequence::NA
- #atom_seq — Bio::PDB::Chain
- #atoms — Bio::PDB::AtomFinder
- #attribute — Bio::GFF::GFF2::Record
- #attributes_to_hash — Bio::GFF::GFF2::Record
- #au — Bio::MEDLINE
- #author — Bio::AAindex
- #author — Bio::LITDB
- #authors — Bio::MEDLINE
- #authors — Bio::PDB
- #auto — Bio::Sequence
- #autodetect — Bio::FlatFile
- #autodetect — Bio::FlatFile::AutoDetect
- #autodetect_flatfile — Bio::FlatFile::AutoDetect
- #ba — Bio::TRANSFAC::MATRIX
- #basecount — Bio::GenBank
- #bc — Bio::TRANSFAC::GENE
- #bdb_open — Bio::FlatFileIndex::DataBank
- #bellman_ford — Bio::Pathway
- #bf — Bio::TRANSFAC::MATRIX
- #bf — Bio::TRANSFAC::SITE
- #bf — Bio::TRANSFAC::CLASS
- #bfs — Bio::Pathway
- #bfs_shortest_path — Bio::Pathway
- #bgcolor — Bio::KEGG::KGML::Entry
- #bgcolor= — Bio::KEGG::KGML::Entry
- #bibitem — Bio::Reference
- #bibtex — Bio::Reference
- #bit_score — Bio::Blast::Default::Report::Hit
- #bit_score — Bio::Blast::Report::Hit
- #bit_score — Bio::Fasta::Report::Hit
- #blast — Bio::FastaFormat
- #block_count — Bio::Blat::Report::Hit
- #block_it — Bio::SiRNA::ShRNA
- #block_sizes — Bio::Blat::Report::Hit
- #blocks — Bio::Blat::Report::Hit
- #blunt? — Bio::RestrictionEnzyme::DoubleStranded
- #bootstrap= — Bio::Tree::Node
- #bootstrap_string= — Bio::Tree::Node
- #breadth_first_search — Bio::Pathway
- #bs — Bio::TRANSFAC::FACTOR
- #bs — Bio::TRANSFAC::GENE
- #cache_all — Bio::FlatFileIndex::FileIDs
- #call — Bio::Command::Tmpdir::Remover
- #call_command — Bio::Command
- #call_command_fork — Bio::Command
- #call_command_open3 — Bio::Command
- #call_command_popen — Bio::Command
- #cc — Bio::EMBL
- #cc — Bio::UniProtKB
- #cc — Bio::UniProtKB
- #cc — Bio::PROSITE
- #cc — Bio::TRANSFAC
- #cd — Bio::TRANSFAC::CELL
- #cdna_rep_h_invitational — Bio::Hinv::HitDefinition
- #cdna_splicing_isoform_curation — Bio::Hinv::HitDefinition
- #cds_start — Bio::FANTOM::MaXML::Annotations
- #cds_stop — Bio::FANTOM::MaXML::Annotations
- #cell — Bio::Reference
- #centreOfGravity — Bio::PDB::Utils
- #chains — Bio::PDB::ChainFinder
- #check — Bio::FlatFileIndex::FileID
- #check — Bio::FlatFileIndex::FileIDs
- #check_all — Bio::FlatFileIndex::FileIDs
- #check_consistency — Bio::FlatFileIndex
- #check_consistency — Bio::FlatFileIndex::DataBank
- #check_options — Bio::Meme::Mast
- #chi_square — Bio::ContingencyTable
- #chi_square_element — Bio::ContingencyTable
- #child_nodes — Bio::KEGG::Keggtab
- #children — Bio::Tree
- #chromosome — Bio::KEGG::GENES
- #chromosomes — Bio::KEGG::GENOME
- #circular — Bio::GenBank
- #circular — Bio::GenPept
- #cl — Bio::TRANSFAC::FACTOR
- #cl — Bio::TRANSFAC::CLASS
- #classes — Bio::PAML::Codeml::Model
- #classes — Bio::KEGG::ENZYME
- #classification — Bio::GenBank
- #classification — Bio::PDB
- #clean_all — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #clear — Bio::Tree
- #clear_node — Bio::Tree
- #clear_relations! — Bio::Pathway
- #clique — Bio::Pathway
- #cliquishness — Bio::Pathway
- #cloneids — Bio::FANTOM::MaXML::Sequences
- #close — Bio::FlatFile
- #close — Bio::FlatFileIndex
- #close — Bio::FlatFileIndex::BDBwrapper
- #close — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #close — Bio::FlatFile::BufferedInputStream
- #close — Bio::FlatFileIndex::Template::NameSpace
- #close — Bio::FlatFileIndex::FileID
- #close — Bio::FlatFileIndex::FileIDs
- #close — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #close — Bio::FlatFileIndex::NameSpaces
- #close — Bio::FlatFileIndex::DataBank
- #close! — Bio::Command::Tmpdir
- #close_all — Bio::FlatFileIndex::FileIDs
- #close_all — Bio::FlatFileIndex::NameSpaces
- #close_flatfile — Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- #closed? — Bio::FlatFileIndex
- #cn — Bio::TRANSFAC::FACTOR
- #co — Bio::TRANSFAC::GENE
- #codes — Bio::Sequence::AA
- #codon_usage — Bio::KEGG::GENES
- #codon_usage — Bio::Sequence::NA
- #cofactors — Bio::KEGG::ENZYME
- #collect! — Bio::Alignment::OriginalAlignment
- #collect_align — Bio::Alignment::OriginalAlignment
- #collect_each_site — Bio::Alignment::EnumerableExtension
- #collect_edge! — Bio::Tree
- #collect_node! — Bio::Tree
- #cols — Bio::AAindex2
- #column_sum — Bio::ContingencyTable
- #column_sum_all — Bio::ContingencyTable
- #comment — Bio::AAindex
- #comment — Bio::EMBL
- #comment — Bio::FastaFormat
- #comment — Bio::KEGG::COMPOUND
- #comment — Bio::KEGG::DRUG
- #comment — Bio::KEGG::ENZYME
- #comment — Bio::KEGG::GENOME
- #comment — Bio::KEGG::GLYCAN
- #comment — Bio::PROSITE
- #comment — Bio::TRANSFAC
- #comment — Bio::NCBIDB::Common
- #comment_only? — Bio::GFF::GFF2::Record
- #comments — Bio::GFF::Record
- #comments — Bio::GFF::GFF2::Record
- #comments= — Bio::GFF::Record
- #comments= — Bio::GFF::GFF2::Record
- #common_name — Bio::NCBIDB::Common
- #common_subgraph — Bio::Pathway
- #compact — Bio::Alignment::OriginalAlignment
- #compact! — Bio::Alignment::OriginalAlignment
- #compcheck — Bio::GCG::Msf
- #complement — Bio::SangerChromatogram
- #complement — Bio::Location
- #complement — Bio::Sequence::NA
- #complement — Bio::RestrictionEnzyme::Fragments
- #complement — Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- #complement! — Bio::SangerChromatogram
- #complement! — Bio::Sequence::NA
- #complement? — Bio::Sim4::Report::Hit
- #complement? — Bio::Spidey::Report::Hit
- #complement_to_array_index — Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- #composition — Bio::KEGG::GLYCAN
- #composition — Bio::Sequence::Common
- #compounds — Bio::KEGG::GLYCAN
- #compounds — Bio::KEGG::MODULE
- #compounds — Bio::KEGG::PATHWAY
- #compounds_as_hash — Bio::KEGG::MODULE
- #compounds_as_hash — Bio::KEGG::PATHWAY
- #compounds_as_strings — Bio::KEGG::MODULE
- #compounds_as_strings — Bio::KEGG::PATHWAY
- #concat — Bio::Alignment::OriginalAlignment
- #concat — Bio::Tree
- #concat — Bio::RestrictionEnzyme::DenseIntArray
- #concat — Bio::RestrictionEnzyme::SortedNumArray
- #concat — Bio::Sequence::Common
- #conect — Bio::PDB::ChemicalComponent
- #config — Bio::Meme::Mast
- #consensus_each_site — Bio::Alignment::EnumerableExtension
- #consensus_iupac — Bio::Alignment::SiteMethods
- #consensus_iupac — Bio::Alignment::EnumerableExtension
- #consensus_string — Bio::Alignment::SiteMethods
- #consensus_string — Bio::Alignment::EnumerableExtension
- #contains_marker? — Bio::Map::ActsLikeMap
- #contingency_coefficient — Bio::ContingencyTable
- #continue? — Bio::PDB::Record
- #control_avg — Bio::KEGG::EXPRESSION
- #control_sd — Bio::KEGG::EXPRESSION
- #control_var — Bio::KEGG::EXPRESSION
- #converged? — Bio::Blast::Default::Report
- #converged? — Bio::Blast::Default::Report::Iteration
- #convert — Bio::TogoWS::REST
- #convert_match — Bio::Alignment::EnumerableExtension
- #convert_nothing — Bio::Sequence::QualityScore::Converter
- #convert_scores_from_phred_to_solexa — Bio::Sequence::QualityScore::Converter
- #convert_scores_from_solexa_to_phred — Bio::Sequence::QualityScore::Converter
- #convert_unmatch — Bio::Alignment::EnumerableExtension
- #correlation_coefficient — Bio::AAindex1
- #count — Bio::NCBI::REST::ESearch::Methods
- #cp — Bio::TRANSFAC::FACTOR
- #crc64 — Bio::Iprscan::Report::Match
- #create_action_at — Bio::RestrictionEnzyme::DoubleStranded
- #create_bins — Bio::RestrictionEnzyme::Range::SequenceRange
- #create_cut_locations — Bio::RestrictionEnzyme::DoubleStranded
- #create_enzyme_actions — Bio::RestrictionEnzyme::Analysis
- #create_primary_and_complement — Bio::RestrictionEnzyme::DoubleStranded
- #cu_list — Bio::KEGG::GENES
- #current — Bio::Reference
- #custom_raise — Bio::SOFT
- #cut — Bio::RestrictionEnzyme::Analysis
- #cut_and_return_by_permutations — Bio::RestrictionEnzyme::Analysis
- #cut_symbol — Bio::RestrictionEnzyme::CutSymbol
- #cut_with_enzyme — Bio::Sequence::NA
- #cut_with_enzymes — Bio::Sequence::NA
- #cut_without_permutations — Bio::RestrictionEnzyme::Analysis
- #dN_dS — Bio::PAML::Codeml::Model
- #dN_dS — Bio::PAML::Codeml::PositiveSite
- #data — Bio::FastaNumericFormat
- #data — Bio::Abif
- #data_class — Bio::EMBL
- #data_source — Bio::FANTOM::MaXML::Annotations
- #data_source — Bio::KEGG::GENOME
- #data_source_coverage — Bio::Hinv::HitDefinition
- #data_source_db_reference_protein_motif_id — Bio::Hinv::HitDefinition
- #data_source_definition — Bio::Hinv::HitDefinition
- #data_source_homologous_species — Bio::Hinv::HitDefinition
- #data_source_identity — Bio::Hinv::HitDefinition
- #data_source_similarity_category — Bio::Hinv::HitDefinition
- #database — Bio::KEGG::Keggtab
- #database_description — Bio::Blast::Remote::Information
- #databases — Bio::Fetch
- #databases — Bio::Blast::Remote::Information
- #datasrc — Bio::FANTOM::MaXML::Annotation
- #date — Bio::Iprscan::Report::Match
- #date — Bio::GenBank
- #date — Bio::GenPept
- #date — Bio::MEDLINE
- #date — Bio::PROSITE
- #date — Bio::TRANSFAC
- #date_created — Bio::EMBL
- #date_modified — Bio::EMBL
- #date_modified — Bio::GenBank
- #db — Bio::Blast::Default::Report
- #db — Bio::Blast::WU::Report
- #db — Bio::Registry
- #db_by_abbrev — Bio::KEGG::Keggtab
- #db_ids — Bio::GO::External2go
- #db_len — Bio::Blast::Report
- #db_num — Bio::Blast::Report
- #db_path — Bio::KEGG::Keggtab
- #db_path_by_abbrev — Bio::KEGG::Keggtab
- #dbclass= — Bio::FlatFile
- #dbclasses — Bio::FlatFile::AutoDetect::RuleRegexp
- #dbclasses — Bio::FlatFile::AutoDetect::RuleProc
- #dblinks — Bio::AAindex
- #dblinks — Bio::EMBL
- #dblinks — Bio::KEGG::COMPOUND
- #dblinks — Bio::KEGG::DRUG
- #dblinks — Bio::KEGG::ENZYME
- #dblinks — Bio::KEGG::GENES
- #dblinks — Bio::KEGG::GLYCAN
- #dblinks — Bio::KEGG::ORTHOLOGY
- #dblinks — Bio::KEGG::PATHWAY
- #dblinks_as_hash — Bio::KEGG::COMPOUND
- #dblinks_as_hash — Bio::KEGG::DRUG
- #dblinks_as_hash — Bio::KEGG::ENZYME
- #dblinks_as_hash — Bio::KEGG::GENES
- #dblinks_as_hash — Bio::KEGG::GLYCAN
- #dblinks_as_hash — Bio::KEGG::ORTHOLOGY
- #dblinks_as_hash — Bio::KEGG::PATHWAY
- #dblinks_as_hash — Bio::KEGG::Common::DblinksAsHash
- #dblinks_as_strings — Bio::KEGG::COMPOUND
- #dblinks_as_strings — Bio::KEGG::DRUG
- #dblinks_as_strings — Bio::KEGG::ENZYME
- #dblinks_as_strings — Bio::KEGG::GENES
- #dblinks_as_strings — Bio::KEGG::GLYCAN
- #dblinks_as_strings — Bio::KEGG::ORTHOLOGY
- #dblinks_as_strings — Bio::KEGG::PATHWAY
- #dbref — Bio::PDB
- #dbs — Bio::GO::External2go
- #dbsource — Bio::GenPept
- #de — Bio::UniProtKB
- #de — Bio::UniProtKB
- #de — Bio::PROSITE
- #de — Bio::TRANSFAC::MATRIX
- #de — Bio::TRANSFAC::SITE
- #de — Bio::TRANSFAC::GENE
- #de — Bio::EMBLDB::Common
- #default_namespaces — Bio::FlatFileIndex
- #default_namespaces= — Bio::FlatFileIndex
- #definition — Bio::Blast::Default::Report::Hit
- #definition — Bio::Blat::Report::Hit
- #definition — Bio::Sim4::Report::Hit
- #definition — Bio::Spidey::Report::Hit
- #definition — Bio::AAindex
- #definition — Bio::KEGG::GENES
- #definition — Bio::KEGG::GENOME
- #definition — Bio::KEGG::MODULE
- #definition — Bio::KEGG::ORTHOLOGY
- #definition — Bio::KEGG::PATHWAY
- #definition — Bio::KEGG::REACTION
- #definition — Bio::PDB
- #definition — Bio::PROSITE
- #definition — Bio::EMBLDB::Common
- #definition — Bio::NCBIDB::Common
- #delete — Bio::Alignment::OriginalAlignment
- #delete — Bio::Blast::NCBIOptions
- #delete — Bio::Pathway
- #delete — Bio::RestrictionEnzyme::DenseIntArray
- #delete — Bio::RestrictionEnzyme::SortedNumArray
- #delete_attribute — Bio::GFF::GFF2::Record
- #delete_attributes — Bio::GFF::GFF2::Record
- #depth_first_search — Bio::Pathway
- #descendents — Bio::Tree
- #descr — Bio::PAML::Codeml::Report
- #description — Bio::Iprscan::Report::Match
- #description — Bio::FastaDefline
- #description — Bio::KEGG::PATHWAY
- #description — Bio::EMBLDB::Common
- #descriptions — Bio::FastaDefline
- #design — Bio::SiRNA
- #design — Bio::SiRNA::ShRNA
- #dfs — Bio::Pathway
- #dfs_topological_sort — Bio::Pathway
- #dijkstra — Bio::Pathway
- #directed — Bio::Pathway
- #directed? — Bio::Pathway
- #direction — Bio::Fasta::Report::Hit
- #disease — Bio::KEGG::GENOME
- #diseases — Bio::KEGG::ENZYME
- #diseases — Bio::KEGG::GENES
- #diseases — Bio::KEGG::PATHWAY
- #diseases_as_hash — Bio::KEGG::GENES
- #diseases_as_hash — Bio::KEGG::PATHWAY
- #diseases_as_hash — Bio::KEGG::Common::DiseasesAsHash
- #diseases_as_strings — Bio::KEGG::GENES
- #diseases_as_strings — Bio::KEGG::PATHWAY
- #distance — Bio::PDB::Coordinate
- #distance — Bio::Tree
- #distance= — Bio::Tree::Edge
- #distance_matrix — Bio::Tree
- #distance_string= — Bio::Tree::Edge
- #division — Bio::EMBL
- #division — Bio::GenBank
- #division — Bio::GenPept
- #division — Bio::KEGG::GENES
- #division — Bio::PROSITE
- #dna — Bio::DAS
- #dna — Bio::Sequence::NA
- #dna! — Bio::Sequence::NA
- #do_align — Bio::Alignment::OriginalAlignment
- #do_parse — Bio::PDB::Record
- #do_parse — Bio::PDB::Record::ATOM
- #doi — Bio::MEDLINE
- #donor_score — Bio::Genscan::Report::Exon
- #down_regulated — Bio::KEGG::EXPRESSION
- #dp — Bio::MEDLINE
- #dr — Bio::UniProtKB
- #dr — Bio::UniProtKB
- #dr — Bio::PROSITE
- #dr — Bio::TRANSFAC::SITE
- #dr — Bio::TRANSFAC::FACTOR
- #dr — Bio::TRANSFAC::CLASS
- #dr — Bio::EMBLDB::Common
- #drug_targets_as_strings — Bio::KEGG::GENES
- #dt — Bio::EMBL
- #dt — Bio::UniProtKB
- #dt — Bio::UniProtKB
- #dt — Bio::PROSITE
- #dt — Bio::TRANSFAC
- #dump_list — Bio::Pathway
- #dump_matrix — Bio::Pathway
- #dump_parameters — Bio::PAML::Common
- #dup — Bio::Alignment::OriginalAlignment
- #each — Bio::Alignment::OriginalAlignment
- #each — Bio::Blast::Default::Report
- #each — Bio::Blast::Default::Report::Iteration
- #each — Bio::Blast::Default::Report::Hit
- #each — Bio::Blast::Report
- #each — Bio::Blast::Report::Iteration
- #each — Bio::Blast::Report::Hit
- #each — Bio::Blat::Report
- #each — Bio::Blat::Report::Hit
- #each — Bio::Fasta::Report
- #each — Bio::HMMER::Report
- #each — Bio::HMMER::Report::Hit
- #each — Bio::Meme::Mast::Report
- #each — Bio::Sim4::Report
- #each — Bio::Sim4::Report::Hit
- #each — Bio::Spidey::Report
- #each — Bio::Spidey::Report::Hit
- #each — Bio::Features
- #each — Bio::References
- #each — Bio::CodonTable
- #each — Bio::FANTOM::MaXML::Sequences
- #each — Bio::FANTOM::MaXML::Annotations
- #each — Bio::FastaNumericFormat
- #each — Bio::PDB
- #each — Bio::PDB::Chain
- #each — Bio::PDB::Model
- #each — Bio::PDB::Residue
- #each — Bio::REBASE
- #each — Bio::Feature
- #each — Bio::DAS::ENTRY_POINT
- #each — Bio::Blast::Fastacmd
- #each — Bio::FlatFile
- #each — Bio::FlatFileIndex::Results
- #each — Bio::FlatFileIndex::FileIDs
- #each — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #each — Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- #each — Bio::Locations
- #each — Bio::RestrictionEnzyme::DenseIntArray
- #each — Bio::RestrictionEnzyme::SortedNumArray
- #each_atom — Bio::PDB::Residue
- #each_atom — Bio::PDB::AtomFinder
- #each_cds — Bio::EMBL
- #each_cds — Bio::GenBank
- #each_chain — Bio::PDB::Model
- #each_chain — Bio::PDB::ChainFinder
- #each_edge — Bio::Tree
- #each_edge_in_path — Bio::Tree
- #each_entry — Bio::Blast::Fastacmd
- #each_entry — Bio::FlatFile
- #each_files — Bio::FlatFileIndex::NameSpaces
- #each_gene — Bio::EMBL
- #each_gene — Bio::GenBank
- #each_hetatm — Bio::PDB::HetatmFinder
- #each_heterogen — Bio::PDB::Chain
- #each_heterogen — Bio::PDB::HeterogenFinder
- #each_hit — Bio::Blast::Default::Report
- #each_hit — Bio::Blast::Report
- #each_hit — Bio::Blat::Report
- #each_hit — Bio::HMMER::Report
- #each_hit — Bio::Sim4::Report
- #each_hit — Bio::Spidey::Report
- #each_hsp — Bio::HMMER::Report::Hit
- #each_iteration — Bio::Blast::Default::Report
- #each_iteration — Bio::Blast::Report
- #each_model — Bio::PDB
- #each_motif — Bio::Meme::Mast::Report
- #each_names — Bio::FlatFileIndex::NameSpaces
- #each_node — Bio::Tree
- #each_out_edge — Bio::Tree
- #each_pair — Bio::Alignment::OriginalAlignment
- #each_residue — Bio::PDB::Chain
- #each_residue — Bio::PDB::ResidueFinder
- #each_rule — Bio::FlatFile::AutoDetect
- #each_seq — Bio::Alignment::OriginalAlignment
- #each_seq — Bio::Alignment::EnumerableExtension
- #each_seq — Bio::Alignment::ArrayExtension
- #each_seq — Bio::Alignment::HashExtension
- #each_site — Bio::Alignment::EnumerableExtension
- #each_site_step — Bio::Alignment::EnumerableExtension
- #each_symbol — Bio::PDB::Record
- #each_window — Bio::Alignment::EnumerableExtension
- #each_with_index — Bio::FlatFileIndex::FileIDs
- #eclinks — Bio::KEGG::GENES
- #edge — Bio::KEGG::KGML::Relation
- #edges — Bio::Pathway
- #edges — Bio::Tree
- #efetch — Bio::NCBI::REST
- #efetch — Bio::PubMed
- #eff_space — Bio::Blast::Report
- #einfo — Bio::NCBI::REST
- #el — Bio::TRANSFAC::SITE
- #elements — Bio::FlatFile::AutoDetect
- #embl — Bio::Reference
- #embl_dr — Bio::UniProtKB
- #embl_dr — Bio::UniProtKB
- #end — Bio::Hinv::KeywordSearch
- #endnote — Bio::Reference
- #entrez_query — Bio::Blast::Report
- #entries — Bio::Alignment::MultiFastaFormat
- #entries — Bio::Alignment::MultiFastaFormat
- #entries — Bio::Alignment::MultiFastaFormat
- #entropy — Bio::Blast::Default::Report
- #entropy — Bio::Blast::Report
- #entry — Bio::Blast::Report::BlastXmlSplitter
- #entry — Bio::Blast::Report::BlastXmlSplitter
- #entry — Bio::EMBL
- #entry — Bio::UniProtKB
- #entry — Bio::UniProtKB
- #entry — Bio::FastaFormat
- #entry — Bio::KEGG::ENZYME
- #entry — Bio::KEGG::GENES
- #entry — Bio::NBRF
- #entry — Bio::TogoWS::REST
- #entry_database_list — Bio::TogoWS::REST
- #entry_ended_pos — Bio::Blast::Report::BlastXmlSplitter
- #entry_ended_pos — Bio::Blast::Report::BlastXmlSplitter
- #entry_ended_pos — Bio::FlatFile
- #entry_id — Bio::Fasta::Report::Hit::Query
- #entry_id — Bio::TargetP::Report
- #entry_id — Bio::DB
- #entry_id — Bio::AAindex
- #entry_id — Bio::EMBL
- #entry_id — Bio::UniProtKB
- #entry_id — Bio::UniProtKB
- #entry_id — Bio::FANTOM::MaXML
- #entry_id — Bio::FANTOM::MaXML::Annotation
- #entry_id — Bio::FastaFormat
- #entry_id — Bio::Fastq
- #entry_id — Bio::GenBank
- #entry_id — Bio::GenPept
- #entry_id — Bio::KEGG::COMPOUND
- #entry_id — Bio::KEGG::DRUG
- #entry_id — Bio::KEGG::ENZYME
- #entry_id — Bio::KEGG::GENES
- #entry_id — Bio::KEGG::GENOME
- #entry_id — Bio::KEGG::GLYCAN
- #entry_id — Bio::KEGG::MODULE
- #entry_id — Bio::KEGG::ORTHOLOGY
- #entry_id — Bio::KEGG::PATHWAY
- #entry_id — Bio::KEGG::REACTION
- #entry_id — Bio::Lasergene
- #entry_id — Bio::LITDB
- #entry_id — Bio::MEDLINE
- #entry_id — Bio::PDB
- #entry_id — Bio::PDB::ChemicalComponent
- #entry_id — Bio::PROSITE
- #entry_id — Bio::TRANSFAC
- #entry_name — Bio::EMBL
- #entry_name — Bio::UniProtKB
- #entry_name — Bio::UniProtKB
- #entry_pos_flag — Bio::FlatFile
- #entry_pos_flag= — Bio::FlatFile
- #entry_raw — Bio::FlatFile
- #entry_start_pos — Bio::Blast::Report::BlastXmlSplitter
- #entry_start_pos — Bio::Blast::Report::BlastXmlSplitter
- #entry_start_pos — Bio::FlatFile
- #entry_version — Bio::EMBL
- #enzyme_name? — Bio::REBASE
- #enzymes — Bio::KEGG::COMPOUND
- #enzymes — Bio::KEGG::GLYCAN
- #enzymes — Bio::KEGG::PATHWAY
- #enzymes — Bio::KEGG::REACTION
- #enzymes — Bio::REBASE
- #enzymes_as_strings — Bio::KEGG::PATHWAY
- #eof? — Bio::FlatFile
- #eof? — Bio::FlatFile::BufferedInputStream
- #eql? — Bio::Relation
- #equals? — Bio::Locations
- #equation — Bio::KEGG::REACTION
- #error_msg — Bio::SOFT
- #error_probabilities — Bio::Fastq
- #errorlog — Bio::ClustalW
- #escape_shell — Bio::Command
- #escape_shell_unix — Bio::Command
- #escape_shell_windows — Bio::Command
- #escaped_cut_symbol — Bio::RestrictionEnzyme::CutSymbol
- #esearch — Bio::NCBI::REST
- #esearch — Bio::PubMed
- #esearch_count — Bio::NCBI::REST
- #est — Bio::NCBI::REST::ESearch::Methods
- #evalue — Bio::Blast::Default::Report::Hit
- #evalue — Bio::Blast::Report::Hit
- #evalue — Bio::Fasta::Report::Hit
- #evalue — Bio::Iprscan::Report::Match
- #events — Bio::Tree::Node
- #evidence — Bio::FANTOM::MaXML::Annotations
- #exec — Bio::EMBOSS
- #exec — Bio::PSORT::CGIDriver
- #exec — Bio::PSORT::PSORT1
- #exec — Bio::PSORT::PSORT2
- #exec — Bio::PTS1
- #exec — Bio::Sim4
- #exec_local — Bio::Sim4
- #exists? — Bio::DB
- #exit_code — Bio::Blast::WU::Report
- #exit_code_message — Bio::Blast::WU::Report
- #exon_type_long — Bio::Genscan::Report::Exon
- #exons — Bio::Blat::Report::Hit
- #exons — Bio::Sim4::Report::Hit
- #exons — Bio::Spidey::Report::Hit
- #expect — Bio::Blast::Report
- #expect — Bio::Blast::WU::Report
- #expected — Bio::ContingencyTable
- #export_tsv — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #fa — Bio::TRANSFAC::FACTOR
- #false_neg — Bio::PROSITE
- #false_negative_hits — Bio::PROSITE
- #false_pos — Bio::PROSITE
- #false_positive_hits — Bio::PROSITE
- #false_positive_sequences — Bio::PROSITE
- #fasta — Bio::FastaFormat
- #fatal_errors — Bio::Blast::WU::Report
- #features — Bio::EMBL
- #features — Bio::DAS
- #features — Bio::NCBIDB::Common
- #fetch — Bio::DB
- #fetch — Bio::Blast::Fastacmd
- #fetch — Bio::Fetch
- #ff — Bio::TRANSFAC::FACTOR
- #fgcolor — Bio::KEGG::KGML::Entry
- #fgcolor= — Bio::KEGG::KGML::Entry
- #fh — Bio::EMBL
- #field — Bio::LITDB
- #fileids — Bio::FlatFileIndex::DataBank
- #filename — Bio::FlatFileIndex::BDBwrapper
- #filename — Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- #filename — Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- #filename — Bio::FlatFileIndex::Template::NameSpace
- #filename — Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- #filename — Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- #filenames — Bio::FlatFileIndex::FileIDs
- #filter — Bio::Blast::Report
- #find_atom — Bio::PDB::AtomFinder
- #find_chain — Bio::PDB::ChainFinder
- #find_hetatm — Bio::PDB::HetatmFinder
- #find_heterogen — Bio::PDB::HeterogenFinder
- #find_match_locations — Bio::RestrictionEnzyme::Analysis
- #find_model — Bio::PDB::ModelFinder
- #find_residue — Bio::PDB::ResidueFinder
- #finder — Bio::PDB::Utils
- #first — Bio::Features
- #first — Bio::Locations
- #first — Bio::RestrictionEnzyme::DenseIntArray
- #first — Bio::RestrictionEnzyme::SortedNumArray
- #first_name — Bio::FastaFormat
- #floyd — Bio::Pathway
- #floyd_warshall — Bio::Pathway
- #for_display — Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- #for_display — Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- #format — Bio::Fastq
- #format — Bio::FlatFileIndex::DataBank
- #format — Bio::Reference
- #format= — Bio::Fasta
- #format= — Bio::Fastq
- #format= — Bio::FlatFileIndex::DataBank
- #format_raw — Bio::Iprscan::Report
- #formats — Bio::Fetch
- #formul — Bio::PDB::ChemicalComponent
- #formula — Bio::KEGG::COMPOUND
- #formula — Bio::KEGG::DRUG
- #forward_complement — Bio::Sequence::NA
- #forward_complement! — Bio::Sequence::NA
- #found_again? — Bio::Blast::Default::Report::Hit
- #fragments — Bio::RestrictionEnzyme::Range::SequenceRange
- #fragments_for_display — Bio::RestrictionEnzyme::Analysis
- #from — Bio::Relation
- #ft — Bio::EMBL
- #ft — Bio::UniProtKB
- #ft — Bio::UniProtKB
- #ft — Bio::TRANSFAC::FACTOR
- #function — Bio::PTS1
- #gap_char — Bio::Alignment::PropertyMethods
- #gap_extend — Bio::Blast::Report
- #gap_length_weight — Bio::GCG::Msf
- #gap_open — Bio::Blast::Report
- #gap_regexp — Bio::Alignment::PropertyMethods
- #gap_weight — Bio::GCG::Msf
- #gapped_entropy — Bio::Blast::Default::Report
- #gapped_kappa — Bio::Blast::Default::Report
- #gapped_lambda — Bio::Blast::Default::Report
- #gbposition — Bio::KEGG::GENES
- #gc_content — Bio::Sequence::NA
- #gc_percent — Bio::Sequence::NA
- #gc_skew — Bio::Sequence::NA
- #gen_ambiguity_map — Bio::CodonTable
- #gene — Bio::KEGG::GENES
- #gene_name — Bio::UniProtKB
- #gene_name — Bio::UniProtKB
- #gene_name — Bio::FANTOM::MaXML::Annotations
- #gene_names — Bio::UniProtKB
- #gene_names — Bio::UniProtKB
- #general — Bio::Reference
- #genes — Bio::KEGG::ENZYME
- #genes — Bio::KEGG::GENES
- #genes — Bio::KEGG::ORTHOLOGY
- #genes — Bio::KEGG::PATHWAY
- #genes_as_hash — Bio::KEGG::ENZYME
- #genes_as_hash — Bio::KEGG::ORTHOLOGY
- #genes_as_hash — Bio::KEGG::PATHWAY
- #genes_as_hash — Bio::KEGG::Common::GenesAsHash
- #genes_as_strings — Bio::KEGG::ENZYME
- #genes_as_strings — Bio::KEGG::ORTHOLOGY
- #genes_as_strings — Bio::KEGG::PATHWAY
- #genome_biol — Bio::Reference
- #genome_res — Bio::Reference
- #genomic — Bio::Spidey::Report::Hit
- #geometricCentre — Bio::PDB::Utils
- #get — Bio::Blast::NCBIOptions
- #get — Bio::DB
- #get — Bio::FANTOM::MaXML::Sequences
- #get — Bio::FastaDefline
- #get — Bio::FlatFileIndex::FileID
- #get_all_by_qualifier — Bio::FANTOM::MaXML::Annotations
- #get_all_by_type — Bio::FastaDefline
- #get_all_property — Bio::Alignment::PropertyMethods
- #get_attribute — Bio::GFF::GFF2::Record
- #get_attributes — Bio::GFF::GFF2::Record
- #get_blocks — Bio::Nexus
- #get_blocks_by_name — Bio::Nexus
- #get_by_id — Bio::Blast::Fastacmd
- #get_by_id — Bio::Fetch
- #get_by_id — Bio::FlatFileIndex
- #get_by_qualifier — Bio::FANTOM::MaXML::Annotations
- #get_by_type — Bio::FastaDefline
- #get_characters_blocks — Bio::Nexus
- #get_characters_string — Bio::Nexus::CharactersBlock
- #get_characters_strings_by_name — Bio::Nexus::CharactersBlock
- #get_data_blocks — Bio::Nexus
- #get_database — Bio::Registry
- #get_datatype — Bio::Nexus::CharactersBlock
- #get_distances_blocks — Bio::Nexus
- #get_dna — Bio::DAS
- #get_dsn — Bio::DAS
- #get_edge — Bio::Tree
- #get_edge_distance — Bio::Tree
- #get_edge_distance_string — Bio::Tree
- #get_edge_merged — Bio::Tree
- #get_entry — Bio::Blast::Report::BlastXmlSplitter
- #get_entry — Bio::Blast::Report::BlastXmlSplitter
- #get_entry — Bio::Blast::RPSBlast::RPSBlastSplitter
- #get_entry — Bio::Blast::RPSBlast::RPSBlastSplitter
- #get_entry — Bio::Fasta::Report::FastaFormat10Splitter
- #get_entry — Bio::Fasta::Report::FastaFormat10Splitter
- #get_entry — Bio::FlatFile::Splitter::Template
- #get_entry — Bio::FlatFile::Splitter::Default
- #get_entry — Bio::FlatFile::Splitter::LineOriented
- #get_entry_points — Bio::DAS
- #get_features — Bio::DAS
- #get_flatfile_data — Bio::FlatFileIndex::DataBank
- #get_gap_character — Bio::Nexus::CharactersBlock
- #get_heterogen_by_id — Bio::PDB::Chain
- #get_match_character — Bio::Nexus::CharactersBlock
- #get_matrix — Bio::Nexus::CharactersBlock
- #get_matrix — Bio::Nexus::DistancesBlock
- #get_max_col — Bio::Nexus::NexusMatrix
- #get_max_row — Bio::Nexus::NexusMatrix
- #get_missing — Bio::Nexus::CharactersBlock
- #get_name — Bio::Nexus::GenericBlock
- #get_name — Bio::Nexus::NexusMatrix
- #get_node_bootstrap — Bio::Tree
- #get_node_bootstrap_string — Bio::Tree
- #get_node_by_name — Bio::Tree
- #get_node_name — Bio::Tree
- #get_number_of_characters — Bio::Nexus::CharactersBlock
- #get_number_of_characters — Bio::Nexus::DistancesBlock
- #get_number_of_taxa — Bio::Nexus::TaxaBlock
- #get_number_of_taxa — Bio::Nexus::CharactersBlock
- #get_number_of_taxa — Bio::Nexus::DistancesBlock
- #get_parsed_entry — Bio::Blast::Report::BlastXmlSplitter
- #get_parsed_entry — Bio::Blast::Report::BlastXmlSplitter
- #get_parsed_entry — Bio::FlatFile::Splitter::Template
- #get_parsed_entry — Bio::FlatFile::Splitter::LineOriented
- #get_record — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #get_residue_by_id — Bio::PDB::Chain
- #get_row_name — Bio::Nexus::CharactersBlock
- #get_row_string — Bio::Nexus::NexusMatrix
- #get_row_strings_by_name — Bio::Nexus::NexusMatrix
- #get_sequence — Bio::ClustalW::Report
- #get_sequence — Bio::ClustalW::Report
- #get_sequence — Bio::Nexus::CharactersBlock
- #get_sequence — Bio::DAS
- #get_sequences_by_name — Bio::Nexus::CharactersBlock
- #get_taxa — Bio::Nexus::TaxaBlock
- #get_taxa — Bio::Nexus::DataBlock
- #get_taxa_blocks — Bio::Nexus
- #get_tokens — Bio::Nexus::GenericBlock
- #get_tree — Bio::Nexus::TreesBlock
- #get_tree_names — Bio::Nexus::TreesBlock
- #get_tree_strings — Bio::Nexus::TreesBlock
- #get_tree_strings_by_name — Bio::Nexus::TreesBlock
- #get_trees_blocks — Bio::Nexus
- #get_trees_by_name — Bio::Nexus::TreesBlock
- #get_triangle — Bio::Nexus::DistancesBlock
- #get_types — Bio::DAS
- #get_value — Bio::Nexus::NexusMatrix
- #getc — Bio::FlatFile::BufferedInputStream
- #gets — Bio::FlatFile
- #gets — Bio::FlatFile::BufferedInputStream
- #gi — Bio::FastaFormat
- #gi — Bio::FastaDefline
- #gi — Bio::NCBIDB::Common
- #glycans — Bio::KEGG::COMPOUND
- #gn — Bio::UniProtKB
- #gn — Bio::UniProtKB
- #go_ids — Bio::GO::External2go
- #go_terms — Bio::Iprscan::Report::Match
- #go_terms — Bio::GO::External2go
- #goid — Bio::GO::GeneAssociation
- #goid2term — Bio::GO::Ontology
- #graph — Bio::PAML::Codeml::PositiveSites
- #graph_omega — Bio::PAML::Codeml::PositiveSites
- #graph_seq — Bio::PAML::Codeml::PositiveSites
- #gss — Bio::NCBI::REST::ESearch::Methods
- #gsub_entities — Bio::FANTOM::MaXML
- #guess — Bio::FlatFile::AutoDetect::RuleTemplate
- #guess — Bio::FlatFile::AutoDetect::RuleDebug
- #guess — Bio::FlatFile::AutoDetect::RuleRegexp
- #guess — Bio::FlatFile::AutoDetect::RuleRegexp2
- #guess — Bio::FlatFile::AutoDetect::RuleProc
- #guess — Bio::Sequence
- #has_gap? — Bio::Alignment::SiteMethods
- #has_key? — Bio::Alignment::OriginalAlignment
- #hash — Bio::Relation
- #hc_between_strands — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #hc_between_strands_as_original_class — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #header — Bio::ClustalW::Report
- #header — Bio::ClustalW::Report
- #height — Bio::KEGG::KGML::Entry
- #height= — Bio::KEGG::KGML::Entry
- #helix — Bio::TMHMM::Report
- #helix — Bio::PDB
- #helper_for_to_array_index — Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- #hetatm — Bio::PDB::Residue
- #hetatm — Bio::PDB::Heterogen
- #hetatms — Bio::PDB::HetatmFinder
- #heterogens — Bio::PDB::HeterogenFinder
- #hetnam — Bio::PDB::ChemicalComponent
- #hetsyn — Bio::PDB::ChemicalComponent
- #hi — Bio::UniProtKB
- #hi — Bio::UniProtKB
- #higher_priority_elements — Bio::FlatFile::AutoDetect::RuleSpecial
- #hit_from — Bio::Sim4::Report::SegmentPair
- #hit_from — Bio::Spidey::Report::SegmentPair
- #hit_id — Bio::Sim4::Report::Hit
- #hit_id — Bio::Spidey::Report::Hit
- #hit_strand — Bio::Spidey::Report::SegmentPair
- #hit_to — Bio::Sim4::Report::SegmentPair
- #hit_to — Bio::Spidey::Report::SegmentPair
- #hits — Bio::Blast::Bl2seq::Report::Iteration
- #hits — Bio::Blast::Default::Report
- #hits — Bio::Blast::Default::Report::Iteration
- #hits — Bio::Blast::Report
- #hits_for_pattern — Bio::Blast::Default::Report::Iteration
- #hits_found_again — Bio::Blast::Default::Report::Iteration
- #hits_newly_found — Bio::Blast::Default::Report::Iteration
- #ho — Bio::TRANSFAC::FACTOR
- #hseq — Bio::Sim4::Report::SegmentPair
- #hseq — Bio::Spidey::Report::SegmentPair
- #hsp_len — Bio::Blast::Report
- #hsps — Bio::Blat::Report::Hit
- #hsps — Bio::Sim4::Report::Hit
- #hsps — Bio::Spidey::Report::Hit
- #http_post — Bio::Command
- #http_post_form — Bio::Command
- #iCode= — Bio::PDB::Residue
- #id — Bio::GFF::GFF3::Record
- #id= — Bio::GFF::GFF3::Record
- #id_line — Bio::EMBL
- #id_line — Bio::UniProtKB
- #id_line — Bio::UniProtKB
- #id_strings — Bio::FANTOM::MaXML::Sequences
- #id_strings — Bio::FANTOM::MaXML::Sequence
- #id_strings — Bio::FastaDefline
- #identifiers — Bio::FastaFormat
- #identity — Bio::Blast::Default::Report::Hit
- #identity — Bio::Blast::Report::Hit
- #identity — Bio::Fasta::Report::Hit
- #illegal_bases — Bio::Sequence::NA
- #import_tsv_files — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #in — Bio::TRANSFAC::FACTOR
- #include? — Bio::FlatFileIndex
- #include? — Bio::FlatFileIndex::Template::NameSpace
- #include? — Bio::Tree
- #include? — Bio::RestrictionEnzyme::DenseIntArray
- #include? — Bio::RestrictionEnzyme::Range::CutRanges
- #include? — Bio::RestrictionEnzyme::Range::HorizontalCutRange
- #include? — Bio::RestrictionEnzyme::Range::VerticalCutRange
- #include? — Bio::RestrictionEnzyme::SortedNumArray
- #include_in_namespaces? — Bio::FlatFileIndex
- #include_in_primary? — Bio::FlatFileIndex
- #inclusion — Bio::Blast::Report
- #index — Bio::Alignment::OriginalAlignment
- #index — Bio::AAindex1
- #index_type= — Bio::FlatFileIndex::DataBank
- #inhibitors — Bio::KEGG::ENZYME
- #init — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #init_fileids — Bio::FlatFileIndex::DataBank
- #init_with_array — Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- #init_with_sorted_tsv_file — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #initialize_copy — Bio::RestrictionEnzyme::DenseIntArray
- #initialize_copy — Bio::RestrictionEnzyme::SortedNumArray
- #initialize_from_string — Bio::PDB::Record
- #initialize_with_pattern_and_cut_locations — Bio::RestrictionEnzyme::DoubleStranded
- #initialize_with_pattern_and_cut_symbols — Bio::RestrictionEnzyme::DoubleStranded
- #initialize_with_rebase — Bio::RestrictionEnzyme::DoubleStranded
- #initiation_score — Bio::Genscan::Report::Exon
- #insert_node — Bio::Tree
- #inspect — Bio::PDB
- #inspect — Bio::PDB::Chain
- #inspect — Bio::PDB::Model
- #inspect — Bio::PDB::Record
- #inspect — Bio::PDB::Residue
- #inspect — Bio::FlatFile::AutoDetect
- #inspect — Bio::FlatFile::AutoDetect::RulesArray
- #inspect — Bio::Tree::Edge
- #inspect — Bio::Tree::Node
- #interleaved? — Bio::Phylip::PhylipFormat
- #internal_data — Bio::RestrictionEnzyme::DenseIntArray
- #internal_data= — Bio::RestrictionEnzyme::DenseIntArray
- #internal_data_hash — Bio::RestrictionEnzyme::SortedNumArray
- #internal_data_hash= — Bio::RestrictionEnzyme::SortedNumArray
- #internal_http — Bio::TogoWS::REST
- #introns — Bio::Sim4::Report::Hit
- #introns — Bio::Spidey::Report::Hit
- #io — Bio::FlatFile
- #ip — Bio::MEDLINE
- #ipr_id — Bio::Iprscan::Report::Match
- #ipr_odescription — Bio::Iprscan::Report::Match
- #is_empty? — Bio::Nexus::NexusMatrix
- #is_gap? — Bio::Alignment::PropertyMethods
- #is_prior_to — Bio::FlatFile::AutoDetect::RuleTemplate
- #isolate — Bio::Alignment::OriginalAlignment
- #issue — Bio::MEDLINE
- #iubmb_reactions — Bio::KEGG::ENZYME
- #journal — Bio::AAindex
- #journal — Bio::LITDB
- #journal — Bio::MEDLINE
- #journal — Bio::NCBI::REST::ESearch::Methods
- #journal — Bio::NCBI::REST::EFetch::Methods
- #jrnl — Bio::PDB
- #kappa — Bio::Blast::Default::Report
- #kappa — Bio::Blast::Report
- #kappa — Bio::PAML::Codeml::Model
- #kcf — Bio::KEGG::COMPOUND
- #kcf — Bio::KEGG::DRUG
- #kcf — Bio::KEGG::GLYCAN
- #kegg_reactions — Bio::KEGG::ENZYME
- #keggclass — Bio::KEGG::GENES
- #keggclass — Bio::KEGG::GLYCAN
- #keggclass — Bio::KEGG::MODULE
- #keggclass — Bio::KEGG::ORTHOLOGY
- #keggclass — Bio::KEGG::PATHWAY
- #keggclasses — Bio::KEGG::GENES
- #keggclasses — Bio::KEGG::ORTHOLOGY
- #keggorg2taxo — Bio::KEGG::Keggtab
- #keggorg2taxonomy — Bio::KEGG::Keggtab
- #keys — Bio::FlatFileIndex::BDBwrapper
- #keys — Bio::FlatFileIndex::FileIDs
- #keyword — Bio::LITDB
- #keywords — Bio::PDB
- #keywords — Bio::EMBLDB::Common
- #keywords — Bio::NCBIDB::Common
- #ko_pathway — Bio::KEGG::PATHWAY
- #korg2taxo — Bio::KEGG::Keggtab
- #korg2taxonomy — Bio::KEGG::Keggtab
- #kruskal — Bio::Pathway
- #kw — Bio::EMBLDB::Common
- #label — Bio::KEGG::KGML::Entry
- #label= — Bio::KEGG::KGML::Entry
- #lambda — Bio::Blast::Default::Report
- #lambda — Bio::Blast::Report
- #lap_at — Bio::Blast::Default::Report::Hit
- #lap_at — Bio::Blast::Report::Hit
- #lap_at — Bio::Fasta::Report::Hit
- #lap_over — Bio::Fasta::Report
- #last — Bio::Features
- #last — Bio::Locations
- #last — Bio::RestrictionEnzyme::DenseIntArray
- #last — Bio::RestrictionEnzyme::SortedNumArray
- #leaves — Bio::Tree
- #left_padding — Bio::RestrictionEnzyme::StringFormatting
- #len — Bio::Blast::Default::Report::Hit
- #len — Bio::Blat::Report::Hit
- #len — Bio::Sim4::Report::Hit
- #len — Bio::Spidey::Report::Hit
- #length — Bio::Fasta::Report::Hit::Query
- #length — Bio::Iprscan::Report::Match
- #length — Bio::Meme::Motif
- #length — Bio::TargetP::Report
- #length — Bio::FastaFormat
- #length — Bio::FastaNumericFormat
- #length — Bio::GenBank
- #length — Bio::GenPept
- #length — Bio::KEGG::GENOME
- #length — Bio::NBRF
- #length — Bio::Locations
- #length — Bio::RestrictionEnzyme::DenseIntArray
- #length — Bio::RestrictionEnzyme::SortedNumArray
- #library_id — Bio::FANTOM::MaXML::Sequence
- #lineage — Bio::KEGG::GENOME
- #list_falsenegative — Bio::PROSITE
- #list_falsepositive — Bio::PROSITE
- #list_output_formats — Bio::Sequence::Format
- #list_potentialhit — Bio::PROSITE
- #list_truepositive — Bio::PROSITE
- #list_unknown — Bio::PROSITE
- #list_xref — Bio::PROSITE
- #lnL — Bio::PAML::Codeml::Model
- #load_parameters — Bio::PAML::Common
- #loc — Bio::TargetP::Report
- #locations — Bio::KEGG::GENES
- #locations — Bio::Feature
- #locus — Bio::FastaFormat
- #locus — Bio::FastaDefline
- #locus — Bio::GenBank
- #locus — Bio::GenPept
- #locus — Bio::NCBIDB::Common
- #log — Bio::ClustalW
- #log — Bio::MAFFT
- #log — Bio::Sim4
- #logy_minus_logx — Bio::KEGG::EXPRESSION
- #lower_priority_elements — Bio::FlatFile::AutoDetect::RuleSpecial
- #lowest_common_ancestor — Bio::Tree
- #lstrip — Bio::Alignment::OriginalAlignment
- #lstrip! — Bio::Alignment::EnumerableExtension
- #ma — Bio::PROSITE
- #ma — Bio::TRANSFAC::MATRIX
- #ma2re — Bio::PROSITE
- #make_cgi_params — Bio::Command
- #make_cgi_params_key_value — Bio::Command
- #make_command_line — Bio::Command
- #make_command_line_options — Bio::Blast::NCBIOptions
- #make_command_line_unix — Bio::Command
- #make_command_line_windows — Bio::Command
- #mapped_to? — Bio::Map::ActsLikeMarker
- #mapping — Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- #mapping — Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- #mapping — Bio::FlatFileIndex::Template::NameSpace
- #mapping — Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- #mapping — Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- #mappings_on — Bio::Map::ActsLikeMarker
- #mask — Bio::Fastq
- #mask_with_enumerator — Bio::Sequence::SequenceMasker
- #mask_with_error_probability — Bio::Sequence::SequenceMasker
- #mask_with_quality_score — Bio::Sequence::SequenceMasker
- #mass — Bio::KEGG::COMPOUND
- #mass — Bio::KEGG::DRUG
- #mass — Bio::KEGG::GLYCAN
- #match — Bio::Blat::Report::Hit
- #match_end — Bio::Iprscan::Report::Match
- #match_line — Bio::ClustalW::Report
- #match_line — Bio::ClustalW::Report
- #match_line — Bio::Alignment::EnumerableExtension
- #match_line_amino — Bio::Alignment::SiteMethods
- #match_line_amino — Bio::Alignment::EnumerableExtension
- #match_line_nuc — Bio::Alignment::SiteMethods
- #match_line_nuc — Bio::Alignment::EnumerableExtension
- #match_start — Bio::Iprscan::Report::Match
- #matrix — Bio::Blast::Report
- #matrix — Bio::AAindex2
- #max — Bio::RestrictionEnzyme::Range::CutRanges
- #max_repeat — Bio::PROSITE
- #max_vertical — Bio::RestrictionEnzyme::Range::CutRanges
- #maxids — Bio::Fetch
- #merge — Bio::Alignment::OriginalAlignment
- #merge! — Bio::Alignment::OriginalAlignment
- #mesh — Bio::MEDLINE
- #message — Bio::Blast::Default::Report
- #message — Bio::Blast::Report
- #method_missing — Bio::Iprscan::Report::Match
- #method_missing — Bio::FastaDefline
- #method_missing — Bio::Registry::DB
- #method_missing — Bio::NCBI::REST::ESearch::Methods
- #method_name — Bio::Iprscan::Report::Match
- #mh — Bio::MEDLINE
- #midline — Bio::Blast::Default::Report::Hit
- #midline — Bio::Blast::Report::Hit
- #milli_bad — Bio::Blat::Report::Hit
- #min — Bio::RestrictionEnzyme::Range::CutRanges
- #min_vertical — Bio::RestrictionEnzyme::Range::CutRanges
- #mismatch — Bio::Blat::Report::Hit
- #missing_char — Bio::Alignment::PropertyMethods
- #missing_mrna_ends — Bio::Spidey::Report::Hit
- #mktmpdir — Bio::Command
- #mm — Bio::TRANSFAC::SITE
- #modelnum — Bio::PAML::Codeml::Model
- #modules — Bio::KEGG::ORTHOLOGY
- #modules — Bio::KEGG::PATHWAY
- #modules_as_hash — Bio::KEGG::ORTHOLOGY
- #modules_as_hash — Bio::KEGG::PATHWAY
- #modules_as_hash — Bio::KEGG::Common::ModulesAsHash
- #modules_as_strings — Bio::KEGG::ORTHOLOGY
- #modules_as_strings — Bio::KEGG::PATHWAY
- #molecular_weight — Bio::Sequence::AA
- #molecular_weight — Bio::Sequence::NA
- #molecule — Bio::EMBL
- #molecule — Bio::UniProtKB
- #molecule — Bio::UniProtKB
- #molecule_type — Bio::EMBL
- #molecule_type — Bio::UniProtKB
- #molecule_type — Bio::UniProtKB
- #moltype — Bio::Fasta::Report::Hit::Query
- #motif — Bio::KEGG::GENES
- #motifs — Bio::KEGG::ENZYME
- #motifs — Bio::KEGG::GENES
- #motifs_as_hash — Bio::KEGG::GENES
- #motifs_as_strings — Bio::KEGG::GENES
- #mrna — Bio::Spidey::Report
- #mrna — Bio::Spidey::Report::Hit
- #mx — Bio::TRANSFAC::FACTOR
- #n_s — Bio::Blat::Report::Hit
- #na — Bio::TRANSFAC::MATRIX
- #na — Bio::Sequence
- #na — Bio::NucleicAcid::Data
- #nalen — Bio::FastaFormat
- #nalen — Bio::Fastq
- #nalen — Bio::GenBank
- #nalen — Bio::KEGG::GENES
- #nalen — Bio::KEGG::GENOME
- #nalen — Bio::NBRF
- #name — Bio::PAML::Codeml::Model
- #name — Bio::TargetP::Report
- #name — Bio::KEGG::COMPOUND
- #name — Bio::KEGG::DRUG
- #name — Bio::KEGG::ENZYME
- #name — Bio::KEGG::GENES
- #name — Bio::KEGG::GENOME
- #name — Bio::KEGG::GLYCAN
- #name — Bio::KEGG::Keggtab
- #name — Bio::KEGG::MODULE
- #name — Bio::KEGG::ORTHOLOGY
- #name — Bio::KEGG::PATHWAY
- #name — Bio::KEGG::REACTION
- #name — Bio::PROSITE
- #name — Bio::AminoAcid::Data
- #name — Bio::NucleicAcid::Data
- #name2one — Bio::AminoAcid::Data
- #name2three — Bio::AminoAcid::Data
- #name= — Bio::FlatFile::AutoDetect::RuleSpecial
- #name_by_abbrev — Bio::KEGG::Keggtab
- #names — Bio::KEGG::COMPOUND
- #names — Bio::KEGG::DRUG
- #names — Bio::KEGG::ENZYME
- #names — Bio::KEGG::GENES
- #names — Bio::KEGG::KGML::Entry
- #names — Bio::KEGG::ORTHOLOGY
- #names — Bio::FlatFileIndex::NameSpaces
- #names — Bio::FlatFileIndex::Indexer::NameSpaces
- #names — Bio::Sequence::AA
- #names — Bio::Sequence::NA
- #names — Bio::AminoAcid::Data
- #names — Bio::NucleicAcid::Data
- #names_as_array — Bio::KEGG::GENES
- #namespaces — Bio::FlatFileIndex
- #nar — Bio::Reference
- #naseq — Bio::GCG::Seq
- #naseq — Bio::EMBL
- #naseq — Bio::FastaFormat
- #naseq — Bio::Fastq
- #naseq — Bio::GenBank
- #naseq — Bio::KEGG::GENES
- #naseq — Bio::NBRF
- #nature — Bio::Reference
- #natype — Bio::GenBank
- #nb_sites — Bio::PAML::Codeml::Report
- #networks_as_strings — Bio::KEGG::GENES
- #new — Bio::Alignment::OriginalAlignment
- #new_http — Bio::Command
- #new_https — Bio::Command
- #newick — Bio::Tree
- #next_entry — Bio::FlatFile
- #nhx_parameters — Bio::Tree::Edge
- #nhx_parameters — Bio::Tree::Node
- #nid — Bio::NCBIDB::Common
- #no_fork? — Bio::Command
- #nodes — Bio::Pathway
- #nodes — Bio::Tree
- #normalize — Bio::Alignment::OriginalAlignment
- #normalize! — Bio::Blast::NCBIOptions
- #normalize! — Bio::Alignment::EnumerableExtension
- #normalize! — Bio::Sequence::Common
- #notes — Bio::Blast::WU::Report
- #notice — Bio::Blast::WU::Report
- #nr — Bio::PROSITE
- #ntlen — Bio::KEGG::GENES
- #ntseq — Bio::EMBL
- #ntseq — Bio::KEGG::GENES
- #nucleotide — Bio::NCBI::REST::EFetch::Methods
- #nucleotide_databases — Bio::Blast::Remote::Information
- #num_codons — Bio::PAML::Codeml::Report
- #num_gene — Bio::KEGG::GENOME
- #num_hits — Bio::Blat::Report
- #num_hits — Bio::Sim4::Report
- #num_hits — Bio::Spidey::Report
- #num_rna — Bio::KEGG::GENOME
- #num_sequences — Bio::PAML::Codeml::Report
- #number_of_edges — Bio::Tree
- #number_of_exons — Bio::Spidey::Report::Hit
- #number_of_nodes — Bio::Tree
- #number_of_sequences — Bio::Alignment::OriginalAlignment
- #number_of_sequences — Bio::Alignment::EnumerableExtension
- #number_of_sequences — Bio::Alignment::ArrayExtension
- #number_of_sequences — Bio::Alignment::HashExtension
- #number_of_splice_sites — Bio::Spidey::Report::Hit
- #obsolete? — Bio::KEGG::ENZYME
- #oc — Bio::TRANSFAC
- #oc — Bio::EMBLDB::Common
- #og — Bio::EMBLDB::Common
- #oh — Bio::UniProtKB
- #oh — Bio::UniProtKB
- #old_matrix — Bio::AAindex2
- #omega — Bio::PAML::Codeml::Model
- #omim — Bio::NCBI::REST::EFetch::Methods
- #one — Bio::AminoAcid::Data
- #one2name — Bio::AminoAcid::Data
- #one2three — Bio::AminoAcid::Data
- #open — Bio::FlatFileIndex::BDBwrapper
- #open — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #open — Bio::FlatFileIndex::FileID
- #open — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #open_flatfile — Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- #open_flatfile — Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- #open_flatfile — Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- #open_flatfile — Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- #option — Bio::Blast
- #option — Bio::ClustalW
- #option — Bio::Fasta
- #option — Bio::HMMER
- #option — Bio::MAFFT
- #option — Bio::Sim4
- #option= — Bio::Blast
- #option= — Bio::Fasta
- #option= — Bio::HMMER
- #options — Bio::Blast::NCBIOptions
- #options — Bio::PAML::Codeml
- #options= — Bio::Blast
- #options= — Bio::PAML::Codeml
- #order — Bio::Alignment::OriginalAlignment
- #org_class — Bio::TRANSFAC
- #org_species — Bio::TRANSFAC
- #organism — Bio::KEGG::GENES
- #organism — Bio::KEGG::GENOME
- #organism — Bio::KEGG::PATHWAY
- #organism — Bio::NCBIDB::Common
- #orientation — Bio::RestrictionEnzyme::SingleStrand
- #orientation — Bio::RestrictionEnzyme::SingleStrandComplement
- #origin — Bio::NCBIDB::Common
- #original_data — Bio::PDB::Record
- #original_databases — Bio::KEGG::GENOME
- #original_db — Bio::KEGG::GENOME
- #orthologs — Bio::KEGG::ENZYME
- #orthologs — Bio::KEGG::GENES
- #orthologs — Bio::KEGG::GLYCAN
- #orthologs — Bio::KEGG::MODULE
- #orthologs — Bio::KEGG::PATHWAY
- #orthologs — Bio::KEGG::REACTION
- #orthologs_as_array — Bio::KEGG::MODULE
- #orthologs_as_hash — Bio::KEGG::ENZYME
- #orthologs_as_hash — Bio::KEGG::GENES
- #orthologs_as_hash — Bio::KEGG::GLYCAN
- #orthologs_as_hash — Bio::KEGG::MODULE
- #orthologs_as_hash — Bio::KEGG::PATHWAY
- #orthologs_as_hash — Bio::KEGG::REACTION
- #orthologs_as_hash — Bio::KEGG::Common::OrthologsAsHash
- #orthologs_as_strings — Bio::KEGG::ENZYME
- #orthologs_as_strings — Bio::KEGG::GENES
- #orthologs_as_strings — Bio::KEGG::GLYCAN
- #orthologs_as_strings — Bio::KEGG::MODULE
- #orthologs_as_strings — Bio::KEGG::PATHWAY
- #orthologs_as_strings — Bio::KEGG::REACTION
- #os — Bio::EMBL
- #os — Bio::UniProtKB
- #os — Bio::UniProtKB
- #os — Bio::TRANSFAC
- #os — Bio::EMBLDB::Common
- #out_degree — Bio::Tree
- #out_edges — Bio::Tree
- #output — Bio::Iprscan::Report
- #output — Bio::Sequence::Format::Formatter::Fasta
- #output — Bio::Sequence::Format::Formatter::Fasta_ncbi
- #output — Bio::Sequence::Format::Formatter::Fasta_numeric
- #output — Bio::Sequence::Format::Formatter::Fastq
- #output — Bio::Sequence::Format::Formatter::Fastq
- #output — Bio::Sequence::Format::FormatterBase
- #output — Bio::Sequence::Format::Formatter::Raw
- #output — Bio::Tree
- #output — Bio::Alignment::Output
- #output — Bio::Sequence::Format
- #output_clustal — Bio::Alignment::Output
- #output_fasta — Bio::Alignment::Output
- #output_fasta — Bio::Sequence::Format
- #output_molphy — Bio::Alignment::Output
- #output_msf — Bio::Alignment::Output
- #output_newick — Bio::Tree
- #output_nhx — Bio::Tree
- #output_phylip — Bio::Alignment::Output
- #output_phylip_distance_matrix — Bio::Tree
- #output_phylipnon — Bio::Alignment::Output
- #overlap — Bio::Blast::Default::Report::Hit
- #overlap — Bio::Blast::Report::Hit
- #overlap — Bio::Fasta::Report::Hit
- #ox — Bio::UniProtKB
- #ox — Bio::UniProtKB
- #p2q — Bio::Sequence::QualityScore::Phred
- #p2q — Bio::Sequence::QualityScore::Solexa
- #pa — Bio::PROSITE
- #pa2re — Bio::PROSITE
- #pages — Bio::MEDLINE
- #palindromic? — Bio::RestrictionEnzyme::SingleStrand
- #parameter_matrix — Bio::Blast::WU::Report
- #parameters — Bio::Blast::WU::Report
- #parent — Bio::Tree
- #parse — Bio::GFF::GFF2
- #parse — Bio::GFF::GFF2::Record
- #parse — Bio::GFF::GFF3
- #parse — Bio::GFF::GFF3::Record
- #parse_enzymes — Bio::REBASE
- #parse_primary — Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- #parse_primary — Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- #parse_references — Bio::REBASE
- #parse_secondary — Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- #parse_suppliers — Bio::REBASE
- #partial — Bio::PROSITE
- #path — Bio::Command::Tmpdir
- #path — Bio::KEGG::Keggtab
- #path — Bio::FlatFile
- #path — Bio::Tree
- #pathway — Bio::KEGG::GENES
- #pathways — Bio::KEGG::COMPOUND
- #pathways — Bio::KEGG::DRUG
- #pathways — Bio::KEGG::ENZYME
- #pathways — Bio::KEGG::GENES
- #pathways — Bio::KEGG::GLYCAN
- #pathways — Bio::KEGG::MODULE
- #pathways — Bio::KEGG::ORTHOLOGY
- #pathways — Bio::KEGG::PATHWAY
- #pathways — Bio::KEGG::REACTION
- #pathways_as_hash — Bio::KEGG::COMPOUND
- #pathways_as_hash — Bio::KEGG::DRUG
- #pathways_as_hash — Bio::KEGG::ENZYME
- #pathways_as_hash — Bio::KEGG::GENES
- #pathways_as_hash — Bio::KEGG::GLYCAN
- #pathways_as_hash — Bio::KEGG::MODULE
- #pathways_as_hash — Bio::KEGG::ORTHOLOGY
- #pathways_as_hash — Bio::KEGG::PATHWAY
- #pathways_as_hash — Bio::KEGG::REACTION
- #pathways_as_hash — Bio::KEGG::Common::PathwaysAsHash
- #pathways_as_strings — Bio::KEGG::COMPOUND
- #pathways_as_strings — Bio::KEGG::DRUG
- #pathways_as_strings — Bio::KEGG::ENZYME
- #pathways_as_strings — Bio::KEGG::GENES
- #pathways_as_strings — Bio::KEGG::GLYCAN
- #pathways_as_strings — Bio::KEGG::MODULE
- #pathways_as_strings — Bio::KEGG::ORTHOLOGY
- #pathways_as_strings — Bio::KEGG::PATHWAY
- #pathways_as_strings — Bio::KEGG::REACTION
- #pathways_in_keggclass — Bio::KEGG::ORTHOLOGY
- #pattern — Bio::Blast::Default::Report
- #pattern — Bio::Blast::Default::Report::Iteration
- #pattern — Bio::Blast::Report
- #pattern — Bio::PROSITE
- #pattern — Bio::RestrictionEnzyme::SingleStrand
- #pattern_positions — Bio::Blast::Default::Report
- #pattern_positions — Bio::Blast::Default::Report::Iteration
- #pdb_xref — Bio::PROSITE
- #pdoc_xref — Bio::PROSITE
- #percent_identity — Bio::Blast::Report::Hit
- #percent_identity — Bio::Blat::Report::Hit
- #percent_identity — Bio::Spidey::Report::Hit
- #permute — Bio::RestrictionEnzyme::Analysis
- #pg — Bio::MEDLINE
- #phred_p2q — Bio::Sequence::QualityScore::Phred
- #phred_q2p — Bio::Sequence::QualityScore::Phred
- #pii — Bio::MEDLINE
- #plasmids — Bio::KEGG::GENOME
- #pmc — Bio::NCBI::REST::EFetch::Methods
- #pmfetch — Bio::PubMed
- #pmid — Bio::MEDLINE
- #pos — Bio::FlatFile
- #pos — Bio::FlatFile::BufferedInputStream
- #pos= — Bio::FlatFile
- #pos= — Bio::FlatFile::BufferedInputStream
- #position — Bio::KEGG::GENES
- #positions_on — Bio::Map::ActsLikeMarker
- #positive — Bio::PROSITE
- #positive_hits — Bio::PROSITE
- #positive_sequences — Bio::PROSITE
- #post — Bio::Command
- #post_form — Bio::Command
- #prefetch_buffer — Bio::FlatFile::BufferedInputStream
- #prefetch_gets — Bio::FlatFile::BufferedInputStream
- #prefetch_readpartial — Bio::FlatFile::BufferedInputStream
- #primary — Bio::FlatFileIndex::DataBank
- #primary — Bio::RestrictionEnzyme::Fragments
- #primary — Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- #primary= — Bio::FlatFileIndex::DataBank
- #primary_namespace — Bio::FlatFileIndex
- #primary_to_array_index — Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- #process — Bio::Lasergene
- #process — Bio::SOFT
- #process_sequences_na — Bio::GFF::GFF3::Record::Gap
- #process_sequences_na_aa — Bio::GFF::GFF3::Record::Gap
- #products — Bio::KEGG::DRUG
- #products — Bio::KEGG::ENZYME
- #profile — Bio::PROSITE
- #program — Bio::Blast::Default::Report
- #protein — Bio::NCBI::REST::EFetch::Methods
- #protein? — Bio::Blat::Report::Hit
- #protein_databases — Bio::Blast::Remote::Information
- #protein_name — Bio::UniProtKB
- #protein_name — Bio::UniProtKB
- #pt — Bio::MEDLINE
- #publication_type — Bio::MEDLINE
- #pubmed — Bio::NCBI::REST::EFetch::Methods
- #pubmed_url — Bio::Reference
- #purge — Bio::Alignment::OriginalAlignment
- #push — Bio::RestrictionEnzyme::DenseIntArray
- #push — Bio::RestrictionEnzyme::SortedNumArray
- #put_record — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #q2p — Bio::Sequence::QualityScore::Phred
- #q2p — Bio::Sequence::QualityScore::Solexa
- #qseq — Bio::Sim4::Report::SegmentPair
- #qseq — Bio::Spidey::Report::SegmentPair
- #qualities — Bio::Fastq
- #quality_score_type — Bio::Fastq
- #quality_score_type — Bio::Sequence::QualityScore::Phred
- #quality_score_type — Bio::Sequence::QualityScore::Solexa
- #quality_scores — Bio::Fastq
- #query — Bio::Alignment::FactoryTemplate::Simple
- #query — Bio::Blast
- #query — Bio::Blat::Report::Hit
- #query — Bio::ClustalW
- #query — Bio::Fasta
- #query — Bio::HMMER
- #query — Bio::MAFFT
- #query — Bio::PAML::Codeml
- #query — Bio::PAML::Common
- #query — Bio::PAML::Yn00
- #query — Bio::Sim4
- #query — Bio::FastaFormat
- #query — Bio::Hinv::KeywordSearch
- #query — Bio::Hinv::IdSearch
- #query — Bio::PubMed
- #query — Bio::Registry
- #query — Bio::Hinv::Common
- #query_align — Bio::Alignment::FactoryTemplate::Simple
- #query_align — Bio::ClustalW
- #query_align — Bio::MAFFT
- #query_alignment — Bio::Alignment::FactoryTemplate::Simple
- #query_alignment — Bio::ClustalW
- #query_alignment — Bio::MAFFT
- #query_by_filename — Bio::Alignment::FactoryTemplate::Simple
- #query_by_filename — Bio::ClustalW
- #query_by_filename — Bio::MAFFT
- #query_by_string — Bio::PAML::Codeml
- #query_by_string — Bio::PAML::Common
- #query_by_string — Bio::PAML::Yn00
- #query_command — Bio::Command
- #query_command_fork — Bio::Command
- #query_command_open3 — Bio::Command
- #query_command_popen — Bio::Command
- #query_def — Bio::Blast::Default::Report
- #query_def — Bio::Blast::RPSBlast::Report
- #query_def — Bio::Blat::Report
- #query_def — Bio::Blat::Report::Hit
- #query_def — Bio::Fasta::Report::Hit
- #query_def — Bio::Sim4::Report
- #query_def — Bio::Sim4::Report::Hit
- #query_def — Bio::Spidey::Report
- #query_def — Bio::Spidey::Report::Hit
- #query_end — Bio::Blast::Default::Report::Hit
- #query_end — Bio::Blast::Report::Hit
- #query_end — Bio::Fasta::Report::Hit
- #query_from — Bio::HMMER::Report::Hsp
- #query_from — Bio::Sim4::Report::SegmentPair
- #query_from — Bio::Spidey::Report::SegmentPair
- #query_id — Bio::Blat::Report
- #query_id — Bio::Blat::Report::Hit
- #query_id — Bio::Fasta::Report::Hit
- #query_id — Bio::Iprscan::Report::Match
- #query_id — Bio::Sim4::Report
- #query_id — Bio::Sim4::Report::Hit
- #query_id — Bio::Spidey::Report
- #query_id — Bio::Spidey::Report::Hit
- #query_len — Bio::Blast::Default::Report
- #query_len — Bio::Blast::RPSBlast::Report
- #query_len — Bio::Blat::Report
- #query_len — Bio::Blat::Report::Hit
- #query_len — Bio::Fasta::Report::Hit
- #query_len — Bio::Sim4::Report
- #query_len — Bio::Sim4::Report::Hit
- #query_len — Bio::Spidey::Report
- #query_len — Bio::Spidey::Report::Hit
- #query_len — Bio::TargetP::Report
- #query_pairwise — Bio::Sim4
- #query_record_number — Bio::Blast::WU::Report
- #query_seq — Bio::Blast::Default::Report::Hit
- #query_seq — Bio::Blast::Report::Hit
- #query_seq — Bio::Fasta::Report::Hit
- #query_seq — Bio::HMMER::Report::Hsp
- #query_start — Bio::Blast::Default::Report::Hit
- #query_start — Bio::Blast::Report::Hit
- #query_start — Bio::Fasta::Report::Hit
- #query_strand — Bio::Spidey::Report::SegmentPair
- #query_string — Bio::Alignment::FactoryTemplate::Simple
- #query_string — Bio::ClustalW
- #query_string — Bio::MAFFT
- #query_to — Bio::HMMER::Report::Hsp
- #query_to — Bio::Sim4::Report::SegmentPair
- #query_to — Bio::Spidey::Report::SegmentPair
- #query_type — Bio::Fasta::Report::Hit
- #ra — Bio::TRANSFAC
- #randomize — Bio::Sequence::Common
- #range — Bio::Genscan::Report::Exon
- #range — Bio::Location
- #range — Bio::Locations
- #raw= — Bio::FlatFile
- #raw_to_reference — Bio::REBASE
- #rc — Bio::TargetP::Report
- #rd — Bio::Reference
- #re — Bio::PROSITE
- #re — Bio::TRANSFAC::SITE
- #re_cut_symbol — Bio::RestrictionEnzyme::CutSymbol
- #re_cut_symbol_adjacent — Bio::RestrictionEnzyme::CutSymbol
- #reaction — Bio::KEGG::ENZYME
- #reactions — Bio::KEGG::COMPOUND
- #reactions — Bio::KEGG::GLYCAN
- #reactions — Bio::KEGG::MODULE
- #reactions — Bio::KEGG::PATHWAY
- #reactions_as_hash — Bio::KEGG::MODULE
- #reactions_as_hash — Bio::KEGG::PATHWAY
- #reactions_as_strings — Bio::KEGG::MODULE
- #reactions_as_strings — Bio::KEGG::PATHWAY
- #read — Bio::FlatFileIndex::FileID
- #read_uri — Bio::Command
- #recalc — Bio::FlatFileIndex::FileID
- #recalc — Bio::FlatFileIndex::FileIDs
- #recalc_all — Bio::FlatFileIndex::FileIDs
- #record — Bio::PDB
- #record — Bio::PDB::ChemicalComponent
- #record_name — Bio::PDB::Record
- #record_size — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #record_type — Bio::PDB::Record
- #records — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #records — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #ref — Bio::UniProtKB
- #ref — Bio::UniProtKB
- #ref — Bio::EMBLDB::Common
- #ref_authors — Bio::TRANSFAC
- #ref_data — Bio::TRANSFAC
- #ref_no — Bio::TRANSFAC
- #ref_title — Bio::TRANSFAC
- #reference — Bio::Blast::Default::Report
- #reference — Bio::LITDB
- #reference — Bio::MEDLINE
- #references — Bio::Blast::Default::Report
- #references — Bio::UniProtKB
- #references — Bio::UniProtKB
- #references — Bio::KEGG::GENOME
- #references — Bio::KEGG::GLYCAN
- #references — Bio::KEGG::ORTHOLOGY
- #references — Bio::KEGG::PATHWAY
- #references — Bio::EMBLDB::Common
- #references — Bio::NCBIDB::Common
- #references — Bio::KEGG::Common::References
- #regulated — Bio::KEGG::EXPRESSION
- #rehash — Bio::Alignment::OriginalAlignment
- #rehash — Bio::PDB::Chain
- #rehash — Bio::PDB::Model
- #rehash — Bio::FlatFile::AutoDetect
- #rehash_heterogens — Bio::PDB::Chain
- #rehash_residues — Bio::PDB::Chain
- #rel_pathways — Bio::KEGG::PATHWAY
- #rel_pathways_as_hash — Bio::KEGG::PATHWAY
- #rel_pathways_as_strings — Bio::KEGG::PATHWAY
- #relation — Bio::Relation
- #relative — Bio::Locations
- #release — Bio::PROSITE
- #release_created — Bio::EMBL
- #release_modified — Bio::EMBL
- #remark — Bio::KEGG::COMPOUND
- #remark — Bio::KEGG::DRUG
- #remark — Bio::KEGG::GLYCAN
- #remark — Bio::PDB
- #removeSolvent — Bio::PDB::Model
- #remove_all_gaps — Bio::Alignment::OriginalAlignment
- #remove_all_gaps! — Bio::Alignment::EnumerableExtension
- #remove_edge — Bio::Tree
- #remove_edge_if — Bio::Tree
- #remove_entry_secure — Bio::Command
- #remove_gaps! — Bio::Alignment::SiteMethods
- #remove_incomplete_cuts — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #remove_node — Bio::Tree
- #remove_node_if — Bio::Tree
- #remove_nonsense_nodes — Bio::Tree
- #remove_seq — Bio::Alignment::OriginalAlignment
- #rep_accession_no — Bio::Hinv::HixRepresent
- #rep_h_invitational_id — Bio::Hinv::HixRepresent
- #rep_match — Bio::Blat::Report::Hit
- #reparse — Bio::Newick
- #replace — Bio::Location
- #replace_attributes — Bio::GFF::GFF2::Record
- #replace_slice — Bio::Alignment::OriginalAlignment
- #report — Bio::SiRNA::Pair
- #report — Bio::SiRNA::ShRNA
- #representative_annotations — Bio::FANTOM::MaXML::Cluster
- #representative_clone — Bio::FANTOM::MaXML::Cluster
- #representative_cloneid — Bio::FANTOM::MaXML::Cluster
- #representative_seqid — Bio::FANTOM::MaXML::Cluster
- #representative_sequence — Bio::FANTOM::MaXML::Cluster
- #resSeq= — Bio::PDB::Residue
- #reset — Bio::Alignment::FactoryTemplate::Simple
- #reset — Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- #reset — Bio::ClustalW
- #reset — Bio::MAFFT
- #reset — Bio::Blast::Remote::Information
- #residues — Bio::PDB::ResidueFinder
- #result — Bio::Hinv::Acc2hit
- #result — Bio::Hinv::Hit2acc
- #result — Bio::Hinv::HitCnt
- #result — Bio::Hinv::HitDefinition
- #result — Bio::Hinv::HitPubmedId
- #result — Bio::Hinv::HitXML
- #result — Bio::Hinv::Hix2hit
- #result — Bio::Hinv::HixCnt
- #result — Bio::Hinv::HixRepresent
- #result — Bio::Hinv::KeywordSearch
- #retrieve — Bio::TogoWS::REST
- #reverse_complement — Bio::Sequence::NA
- #reverse_complement! — Bio::Sequence::NA
- #reverse_each — Bio::RestrictionEnzyme::DenseIntArray
- #reverse_each — Bio::RestrictionEnzyme::SortedNumArray
- #revtrans — Bio::CodonTable
- #rewind — Bio::Blast::Report::BlastXmlSplitter
- #rewind — Bio::Blast::Report::BlastXmlSplitter
- #rewind — Bio::Blast::RPSBlast::RPSBlastSplitter
- #rewind — Bio::Blast::RPSBlast::RPSBlastSplitter
- #rewind — Bio::FlatFile
- #rewind — Bio::FlatFile::BufferedInputStream
- #rewind — Bio::FlatFile::Splitter::Template
- #rewind — Bio::FlatFile::Splitter::LineOriented
- #reynolds — Bio::SiRNA
- #reynolds? — Bio::SiRNA
- #right_padding — Bio::RestrictionEnzyme::StringFormatting
- #rl — Bio::TRANSFAC
- #rn — Bio::TRANSFAC
- #rna — Bio::Sequence::NA
- #rna! — Bio::Sequence::NA
- #rna? — Bio::Sequence::NA
- #row_sum — Bio::ContingencyTable
- #row_sum_all — Bio::ContingencyTable
- #rows — Bio::AAindex2
- #rpairs — Bio::KEGG::COMPOUND
- #rpairs — Bio::KEGG::REACTION
- #rpairs_as_hash — Bio::KEGG::REACTION
- #rpairs_as_strings — Bio::KEGG::REACTION
- #rpairs_as_tokens — Bio::KEGG::REACTION
- #rstrip — Bio::Alignment::OriginalAlignment
- #rstrip! — Bio::Alignment::EnumerableExtension
- #rt — Bio::TRANSFAC
- #ru — Bio::PROSITE
- #rule — Bio::PROSITE
- #run — Bio::Meme::Mast
- #run — Bio::PAML::Common
- #s1 — Bio::TRANSFAC::SITE
- #safe_command_line_array — Bio::Command
- #save_yaml — Bio::REBASE
- #sc — Bio::TRANSFAC::FACTOR
- #sc_match — Bio::Blast::Report
- #sc_mismatch — Bio::Blast::Report
- #science — Bio::Reference
- #score — Bio::Blast::Default::Report::Hit
- #score — Bio::Blast::WU::Report::Hit
- #score — Bio::Blat::Report::Hit
- #scores2str — Bio::Fastq::FormatData
- #sd — Bio::TRANSFAC::CLASS
- #sd — Bio::TRANSFAC::GENE
- #search — Bio::FlatFileIndex
- #search — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #search — Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- #search — Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- #search — Bio::FlatFileIndex::Template::NameSpace
- #search — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #search — Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- #search — Bio::FlatFileIndex::NameSpaces
- #search — Bio::PubMed
- #search — Bio::TogoWS::REST
- #search — Bio::NCBI::REST::ESearch::Methods
- #search_all — Bio::FlatFileIndex::DataBank
- #search_all_get_unique_id — Bio::FlatFileIndex::DataBank
- #search_database_list — Bio::TogoWS::REST
- #search_names — Bio::FlatFileIndex::NameSpaces
- #search_namespaces — Bio::FlatFileIndex
- #search_namespaces — Bio::FlatFileIndex::DataBank
- #search_namespaces_get_unique_id — Bio::FlatFileIndex::DataBank
- #search_primary — Bio::FlatFileIndex
- #search_primary — Bio::FlatFileIndex::DataBank
- #search_primary_get_unique_id — Bio::FlatFileIndex::DataBank
- #secondary — Bio::FlatFileIndex::DataBank
- #secondary= — Bio::FlatFileIndex::DataBank
- #secondary_namespaces — Bio::FlatFileIndex
- #seek — Bio::FlatFileIndex::FileID
- #seek — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #segment — Bio::NCBIDB::Common
- #segmentpairs — Bio::Sim4::Report::Hit
- #segmentpairs — Bio::Spidey::Report::Hit
- #select — Bio::Alignment::OriginalAlignment
- #seq — Bio::GCG::Seq
- #seq — Bio::EMBL
- #seq — Bio::UniProtKB
- #seq — Bio::UniProtKB
- #seq — Bio::FastaFormat
- #seq — Bio::Fastq
- #seq — Bio::GenBank
- #seq — Bio::GenPept
- #seq — Bio::Lasergene
- #seq — Bio::NBRF
- #seq — Bio::SangerChromatogram
- #seq — Bio::Sequence::Common
- #seq! — Bio::Sequence::Common
- #seq_class — Bio::NBRF
- #seq_data — Bio::GCG::Msf
- #seq_len — Bio::GenBank
- #seq_len — Bio::GenPept
- #seq_length — Bio::Alignment::EnumerableExtension
- #seqclass — Bio::Alignment::PropertyMethods
- #seqclass — Bio::Alignment::EnumerableExtension
- #seqlen — Bio::EMBL
- #seqres — Bio::PDB
- #sequence — Bio::FANTOM::MaXML::Cluster
- #sequence — Bio::NCBI::REST::EFetch::Methods
- #sequence_length — Bio::EMBL
- #sequence_length — Bio::UniProtKB
- #sequence_length — Bio::UniProtKB
- #sequence_names — Bio::Alignment::EnumerableExtension
- #sequence_names — Bio::Alignment::HashExtension
- #sequence_string — Bio::SangerChromatogram
- #sequences — Bio::FANTOM::MaXML::Cluster
- #server= — Bio::Blast
- #set — Bio::Blast::NCBIOptions
- #set_RN — Bio::UniProtKB
- #set_RN — Bio::UniProtKB
- #set_aaseq — Bio::Genscan::Report::Gene
- #set_alignment — Bio::HMMER::Report::Hsp
- #set_all_property — Bio::Alignment::PropertyMethods
- #set_attribute — Bio::GFF::GFF2::Record
- #set_cut_symbol — Bio::RestrictionEnzyme::CutSymbol
- #set_datatype — Bio::Nexus::CharactersBlock
- #set_date — Bio::GO::External2go
- #set_default_parameters — Bio::PAML::Common
- #set_desc — Bio::GO::External2go
- #set_features — Bio::PSORT::PSORT2::Report
- #set_gap_character — Bio::Nexus::CharactersBlock
- #set_header_line — Bio::PSORT::PSORT2::Report
- #set_match_character — Bio::Nexus::CharactersBlock
- #set_matrix — Bio::Nexus::CharactersBlock
- #set_matrix — Bio::Nexus::DistancesBlock
- #set_missing — Bio::Nexus::CharactersBlock
- #set_naseq — Bio::Genscan::Report::Gene
- #set_number_of_characters — Bio::Nexus::CharactersBlock
- #set_number_of_characters — Bio::Nexus::DistancesBlock
- #set_number_of_taxa — Bio::Nexus::TaxaBlock
- #set_number_of_taxa — Bio::Nexus::CharactersBlock
- #set_number_of_taxa — Bio::Nexus::DistancesBlock
- #set_polyA — Bio::Genscan::Report::Gene
- #set_prediction — Bio::PSORT::PSORT2::Report
- #set_primary_namespace — Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- #set_promoter — Bio::Genscan::Report::Gene
- #set_triangle — Bio::Nexus::DistancesBlock
- #set_value — Bio::Nexus::NexusMatrix
- #setup_enzyme_and_reference_association — Bio::REBASE
- #setup_enzyme_data — Bio::REBASE
- #setup_new_bin — Bio::RestrictionEnzyme::Range::SequenceRange
- #sf — Bio::TRANSFAC::SITE
- #sf — Bio::TRANSFAC::FACTOR
- #shape — Bio::KEGG::KGML::Entry
- #shape= — Bio::KEGG::KGML::Entry
- #sheet — Bio::PDB
- #shift — Bio::Alignment::OriginalAlignment
- #significant — Bio::PAML::Codeml::Report
- #site — Bio::PROSITE
- #sites — Bio::PAML::Codeml::Report
- #size — Bio::Alignment::OriginalAlignment
- #size — Bio::FlatFileIndex::BDB_1::BDBMappingFile
- #size — Bio::FlatFileIndex::Results
- #size — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #size — Bio::Hinv::KeywordSearch
- #size — Bio::Locations
- #size — Bio::RestrictionEnzyme::DenseIntArray
- #size — Bio::RestrictionEnzyme::SortedNumArray
- #skip_flag — Bio::PROSITE
- #skip_leader — Bio::Blast::Report::BlastXmlSplitter
- #skip_leader — Bio::Blast::Report::BlastXmlSplitter
- #skip_leader — Bio::Blast::RPSBlast::RPSBlastSplitter
- #skip_leader — Bio::Blast::RPSBlast::RPSBlastSplitter
- #skip_leader — Bio::Fasta::Report::FastaFormat10Splitter
- #skip_leader — Bio::Fasta::Report::FastaFormat10Splitter
- #skip_leader — Bio::FlatFile::Splitter::Template
- #skip_leader — Bio::FlatFile::Splitter::Default
- #skip_leader — Bio::FlatFile::Splitter::LineOriented
- #skip_spaces — Bio::FlatFile::BufferedInputStream
- #slice — Bio::Alignment::EnumerableExtension
- #small_world — Bio::Pathway
- #so — Bio::MEDLINE
- #so — Bio::TRANSFAC::SITE
- #solexa_p2q — Bio::Sequence::QualityScore::Solexa
- #solexa_q2p — Bio::Sequence::QualityScore::Solexa
- #sort! — Bio::RestrictionEnzyme::DenseIntArray
- #sort! — Bio::RestrictionEnzyme::SortedNumArray
- #sort_attributes_by_tag! — Bio::GFF::GFF2::Record
- #source — Bio::MEDLINE
- #source — Bio::NCBIDB::Common
- #sp_xref — Bio::PROSITE
- #span — Bio::Locations
- #species — Bio::EMBL
- #splice — Bio::Sequence::Common
- #splicing — Bio::Sequence::Common
- #split — Bio::Sequence::Common
- #split_label_value_in — Bio::SOFT
- #sq — Bio::EMBL
- #sq — Bio::UniProtKB
- #sq — Bio::UniProtKB
- #sq — Bio::TRANSFAC::SITE
- #sq — Bio::TRANSFAC::FACTOR
- #ssbond — Bio::PDB
- #st — Bio::TRANSFAC::SITE
- #standard_comment? — Bio::Lasergene
- #start — Bio::Fasta::Report::Hit::Query
- #start — Bio::Hinv::KeywordSearch
- #start_codon? — Bio::CodonTable
- #start_http — Bio::Command
- #start_http_uri — Bio::Command
- #statistics — Bio::Blast::Report
- #statistics — Bio::KEGG::GENOME
- #statistics — Bio::PROSITE
- #status — Bio::Iprscan::Report::Match
- #sticky? — Bio::RestrictionEnzyme::DoubleStranded
- #stop — Bio::Fasta::Report::Hit::Query
- #stop_codon? — Bio::CodonTable
- #store — Bio::Alignment::OriginalAlignment
- #str2scores — Bio::Fastq::FormatData
- #strand — Bio::Blat::Report::Hit
- #strand — Bio::Spidey::Report::Hit
- #strand — Bio::GenBank
- #strandedness — Bio::GenBank
- #strands_for_display — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #strip — Bio::Alignment::OriginalAlignment
- #strip! — Bio::Alignment::EnumerableExtension
- #strip_and_sort — Bio::RestrictionEnzyme::Fragments
- #strip_cuts_and_padding — Bio::RestrictionEnzyme::StringFormatting
- #strip_padding — Bio::RestrictionEnzyme::StringFormatting
- #structure — Bio::KEGG::GENES
- #structures — Bio::KEGG::ENZYME
- #structures — Bio::KEGG::GENES
- #subgraph — Bio::Pathway
- #subseq — Bio::Alignment::EnumerableExtension
- #subseq — Bio::Sequence::Common
- #substrates — Bio::KEGG::ENZYME
- #subtree — Bio::Tree
- #subtree_with_all_paths — Bio::Tree
- #sv — Bio::EMBL
- #sw — Bio::Fasta::Report::Hit
- #swissprot_release_number — Bio::PROSITE
- #swissprot_release_sequences — Bio::PROSITE
- #sy — Bio::TRANSFAC::FACTOR
- #symbol_comparison_table — Bio::GCG::Msf
- #synonyms — Bio::UniProtKB
- #synonyms — Bio::UniProtKB
- #sysname — Bio::KEGG::ENZYME
- #sz — Bio::TRANSFAC::FACTOR
- #ta — Bio::MEDLINE
- #table_sum_all — Bio::ContingencyTable
- #tags — Bio::DB
- #target — Bio::Blat::Report::Hit
- #target_avg — Bio::KEGG::EXPRESSION
- #target_def — Bio::Blast::Default::Report::Hit
- #target_def — Bio::Blat::Report::Hit
- #target_def — Bio::Fasta::Report::Hit
- #target_def — Bio::HMMER::Report::Hit
- #target_def — Bio::Sim4::Report::Hit
- #target_def — Bio::Spidey::Report::Hit
- #target_end — Bio::Blast::Default::Report::Hit
- #target_end — Bio::Blast::Report::Hit
- #target_end — Bio::Fasta::Report::Hit
- #target_from — Bio::HMMER::Report::Hsp
- #target_id — Bio::Blast::Default::Report::Hit
- #target_id — Bio::Blat::Report::Hit
- #target_id — Bio::Fasta::Report::Hit
- #target_id — Bio::Sim4::Report::Hit
- #target_id — Bio::Spidey::Report::Hit
- #target_len — Bio::Blast::Default::Report::Hit
- #target_len — Bio::Blat::Report::Hit
- #target_len — Bio::Fasta::Report::Hit
- #target_len — Bio::Sim4::Report::Hit
- #target_len — Bio::Spidey::Report::Hit
- #target_sd — Bio::KEGG::EXPRESSION
- #target_seq — Bio::Blast::Default::Report::Hit
- #target_seq — Bio::Blast::Report::Hit
- #target_seq — Bio::Fasta::Report::Hit
- #target_seq — Bio::HMMER::Report::Hsp
- #target_start — Bio::Blast::Default::Report::Hit
- #target_start — Bio::Blast::Report::Hit
- #target_start — Bio::Fasta::Report::Hit
- #target_to — Bio::HMMER::Report::Hsp
- #target_type — Bio::Fasta::Report::Hit
- #target_var — Bio::KEGG::EXPRESSION
- #taxa_list — Bio::KEGG::Keggtab
- #taxid — Bio::KEGG::GENOME
- #taxo2keggorgs — Bio::KEGG::Keggtab
- #taxo2korgs — Bio::KEGG::Keggtab
- #taxon2keggorgs — Bio::KEGG::Keggtab
- #taxon2korgs — Bio::KEGG::Keggtab
- #taxon_range — Bio::PROSITE
- #taxonomy — Bio::KEGG::GENOME
- #taxonomy — Bio::KEGG::Keggtab
- #taxonomy — Bio::NCBIDB::Common
- #taxonomy — Bio::NCBI::REST::EFetch::Methods
- #termination_score — Bio::Genscan::Report::Exon
- #three — Bio::AminoAcid::Data
- #three2name — Bio::AminoAcid::Data
- #three2one — Bio::AminoAcid::Data
- #threshold — Bio::Fasta::Report
- #ti — Bio::MEDLINE
- #title — Bio::AAindex
- #title — Bio::LITDB
- #title — Bio::MEDLINE
- #to — Bio::Relation
- #to_1 — Bio::AminoAcid::Data
- #to_3 — Bio::AminoAcid::Data
- #to_a — Bio::ClustalW::Report
- #to_a — Bio::MAFFT::Report
- #to_a — Bio::PAML::Codeml::PositiveSite
- #to_a — Bio::ClustalW::Report
- #to_a — Bio::FANTOM::MaXML::Sequences
- #to_a — Bio::FANTOM::MaXML::Annotations
- #to_a — Bio::GFF::GFF2::Record::Value
- #to_a — Bio::PDB::Record::ATOM
- #to_a — Bio::FlatFileIndex::Results
- #to_a — Bio::RestrictionEnzyme::SortedNumArray
- #to_array_index — Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- #to_array_index — Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- #to_ary — Bio::PDB::Coordinate
- #to_biosequence — Bio::EMBL
- #to_biosequence — Bio::FastaFormat
- #to_biosequence — Bio::FastaNumericFormat
- #to_biosequence — Bio::Fastq
- #to_biosequence — Bio::GenBank
- #to_biosequence — Bio::SangerChromatogram
- #to_clustal — Bio::Alignment::Output
- #to_fasta — Bio::Alignment::OriginalAlignment
- #to_fasta — Bio::ClustalW::Report
- #to_fasta — Bio::MAFFT::Report
- #to_fasta — Bio::ClustalW::Report
- #to_fasta — Bio::Sequence::Common
- #to_fasta_array — Bio::Alignment::OriginalAlignment
- #to_fastaformat_array — Bio::Alignment::OriginalAlignment
- #to_hash — Bio::Alignment::OriginalAlignment
- #to_hash — Bio::Iprscan::Report
- #to_hash — Bio::Feature
- #to_io — Bio::FlatFile
- #to_io — Bio::FlatFile::BufferedInputStream
- #to_list — Bio::Pathway
- #to_matrix — Bio::Pathway
- #to_nexus — Bio::Nexus::GenericBlock
- #to_nexus — Bio::Nexus::TaxaBlock
- #to_nexus — Bio::Nexus::CharactersBlock
- #to_nexus — Bio::Nexus::DataBlock
- #to_nexus — Bio::Nexus::DistancesBlock
- #to_nexus — Bio::Nexus::TreesBlock
- #to_nexus_row_array — Bio::Nexus::NexusMatrix
- #to_re — Bio::Sequence::AA
- #to_re — Bio::Sequence::NA
- #to_re — Bio::AminoAcid::Data
- #to_re — Bio::NucleicAcid::Data
- #to_relations — Bio::Pathway
- #to_s — Bio::Blast::Default::Report
- #to_s — Bio::PAML::Codeml::Model
- #to_s — Bio::PAML::Codeml::PositiveSites
- #to_s — Bio::TMHMM::Report
- #to_s — Bio::TMHMM::TMH
- #to_s — Bio::FANTOM::MaXML
- #to_s — Bio::FastaFormat
- #to_s — Bio::FastaDefline
- #to_s — Bio::Fastq
- #to_s — Bio::GFF::GFF2
- #to_s — Bio::GFF::GFF2::Record
- #to_s — Bio::GFF::GFF2::Record::Value
- #to_s — Bio::GFF::GFF2::MetaData
- #to_s — Bio::GFF::GFF3
- #to_s — Bio::GFF::GFF3::SequenceRegion
- #to_s — Bio::GFF::GFF3::Record
- #to_s — Bio::GFF::GFF3::Record::Target
- #to_s — Bio::GFF::GFF3::Record::Gap
- #to_s — Bio::GFF::GFF3::Record::Gap::Code
- #to_s — Bio::GFF::GFF3::RecordBoundary
- #to_s — Bio::NBRF
- #to_s — Bio::Nexus
- #to_s — Bio::Nexus::GenericBlock
- #to_s — Bio::Nexus::NexusMatrix
- #to_s — Bio::PDB
- #to_s — Bio::PDB::Chain
- #to_s — Bio::PDB::Model
- #to_s — Bio::PDB::Record::ATOM
- #to_s — Bio::PDB::Residue
- #to_s — Bio::FlatFileIndex::Results
- #to_s — Bio::FlatFileIndex::FileID
- #to_s — Bio::FlatFileIndex::Flat_1::Record
- #to_s — Bio::FlatFileIndex::NameSpaces
- #to_s — Bio::FlatFileIndex::DataBank
- #to_s — Bio::Locations
- #to_s — Bio::Sequence
- #to_s — Bio::Tree::Edge
- #to_s — Bio::Tree::Node
- #to_s — Bio::Sequence::Common
- #to_seq — Bio::FastaFormat
- #to_seq — Bio::FastaNumericFormat
- #to_seq — Bio::SangerChromatogram
- #to_str — Bio::GO::GeneAssociation
- #to_str — Bio::GO::External2go
- #to_str — Bio::Nexus
- #to_str — Bio::Nexus::GenericBlock
- #to_str — Bio::Nexus::NexusMatrix
- #to_str — Bio::Sequence
- #to_str — Bio::Sequence::Common
- #topology — Bio::EMBL
- #total — Bio::PROSITE
- #total — Bio::Sequence::Common
- #total_distance — Bio::Tree
- #total_hits — Bio::PROSITE
- #total_sequences — Bio::PROSITE
- #tr — Bio::TRANSFAC::GENE
- #translate — Bio::Sequence::NA
- #tree — Bio::PAML::Codeml::Model
- #tree — Bio::Newick
- #tree_length — Bio::PAML::Codeml::Model
- #trends — Bio::Reference
- #tsort_each_child — Bio::FlatFile::AutoDetect
- #tsort_each_node — Bio::FlatFile::AutoDetect
- #turn — Bio::PDB
- #ty — Bio::TRANSFAC::SITE
- #ui — Bio::MEDLINE
- #uitei — Bio::SiRNA
- #uitei? — Bio::SiRNA
- #undirected — Bio::Pathway
- #undirected? — Bio::Pathway
- #ungetc — Bio::FlatFile::BufferedInputStream
- #ungets — Bio::FlatFile::BufferedInputStream
- #uniq! — Bio::RestrictionEnzyme::DenseIntArray
- #uniq! — Bio::RestrictionEnzyme::SortedNumArray
- #unknown — Bio::PROSITE
- #unknown_hits — Bio::PROSITE
- #unknown_sequences — Bio::PROSITE
- #unshift — Bio::Alignment::OriginalAlignment
- #unshift — Bio::RestrictionEnzyme::DenseIntArray
- #unshift — Bio::RestrictionEnzyme::SortedNumArray
- #up_regulated — Bio::KEGG::EXPRESSION
- #val2rgb — Bio::KEGG::EXPRESSION
- #validate_1 — Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- #validate_2 — Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- #validate_2 — Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- #validate_args — Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- #validate_args — Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- #validate_args — Bio::RestrictionEnzyme::SingleStrand
- #validate_checksum — Bio::GCG::Msf
- #validate_checksum — Bio::GCG::Seq
- #validate_cut_locations — Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- #validate_format — Bio::Fastq
- #values — Bio::Alignment::OriginalAlignment
- #values — Bio::GFF::GFF2::Record::Value
- #vc_complement — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #vc_complement_as_original_class — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #vc_primary — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #vc_primary_as_original_class — Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- #vernacular_name — Bio::NCBIDB::Common
- #version — Bio::Blast::Default::Report
- #version — Bio::EMBL
- #version — Bio::PDB
- #version — Bio::NCBIDB::Common
- #version_date — Bio::Blast::Default::Report
- #version_number — Bio::Blast::Default::Report
- #versions — Bio::NCBIDB::Common
- #vertical_min_max_helper — Bio::RestrictionEnzyme::Range::CutRanges
- #vi — Bio::MEDLINE
- #volume — Bio::LITDB
- #volume — Bio::MEDLINE
- #w — Bio::PAML::Codeml::PositiveSite
- #warnings — Bio::Blast::WU::Report
- #warnings — Bio::Blast::WU::Report::Iteration
- #weight — Bio::AminoAcid::Data
- #weight — Bio::NucleicAcid::Data
- #width — Bio::KEGG::KGML::Entry
- #width= — Bio::KEGG::KGML::Entry
- #window — Bio::Alignment::EnumerableExtension
- #window_search — Bio::Sequence::Common
- #windows_platform? — Bio::Command
- #with_cut_symbols — Bio::RestrictionEnzyme::SingleStrand
- #with_spaces — Bio::RestrictionEnzyme::SingleStrand
- #words — Bio::FastaDefline
- #write — Bio::FlatFileIndex::DataBank
- #write_record — Bio::FlatFileIndex::Flat_1::FlatMappingFile
- #writeback_array — Bio::FlatFileIndex::BDBwrapper
- #x — Bio::KEGG::KGML::Entry
- #x — Bio::PDB::Coordinate
- #x= — Bio::KEGG::KGML::Entry
- #x= — Bio::PDB::Coordinate
- #xyz — Bio::PDB::Coordinate
- #xyz — Bio::PDB::Record::ATOM
- #y — Bio::KEGG::KGML::Entry
- #y — Bio::PDB::Coordinate
- #y= — Bio::KEGG::KGML::Entry
- #y= — Bio::PDB::Coordinate
- #year — Bio::MEDLINE
- #z — Bio::PDB::Coordinate
- #z= — Bio::PDB::Coordinate